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Ronnie Alves (Ed.)
Advances
LNBI 11228
in Bioinformatics and
Computational Biology
11th Brazilian Symposium on Bioinformatics, BSB 2018
Niterói, Brazil, October 30 – November 1, 2018
Proceedings
123
Lecture Notes in Bioinformatics 11228
Subseries of Lecture Notes in Computer Science
LNBI Series Editors

Sorin Istrail
Brown University, Providence, RI, USA
Pavel Pevzner
University of California, San Diego, CA, USA
Michael Waterman
University of Southern California, Los Angeles, CA, USA
LNBI Editorial Board

Søren Brunak
Technical University of Denmark, Kongens Lyngby, Denmark
Mikhail S. Gelfand
IITP, Research and Training Center on Bioinformatics, Moscow, Russia
Thomas Lengauer
Max Planck Institute for Informatics, Saarbrücken, Germany
Satoru Miyano
University of Tokyo, Tokyo, Japan
Eugene Myers
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden,
Germany
Marie-France Sagot
Université Lyon 1, Villeurbanne, France
David Sankoff
University of Ottawa, Ottawa, Canada
Ron Shamir
Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
Terry Speed
Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
Martin Vingron
Max Planck Institute for Molecular Genetics, Berlin, Germany
W. Eric Wong
University of Texas at Dallas, Richardson, TX, USA
More information about this series at http://www.springer.com/series/5381
Ronnie Alves (Ed.)
Advances
in Bioinformatics and
Computational Biology
11th Brazilian Symposium on Bioinformatics, BSB 2018
Niterói, Brazil, October 30 – November 1, 2018
Proceedings
123
Editor
Ronnie Alves
Instituto Tecnológico Vale
Belém
Brazil
ISSN 0302-9743 ISSN 1611-3349 (electronic)

Lecture Notes in Bioinformatics
ISBN 978-3-030-01721-7 ISBN 978-3-030-01722-4 (eBook)
https://doi.org/10.1007/978-3-030-01722-4
Library of Congress Control Number: 2018956561
LNCS Sublibrary: SL8 – Bioinformatics
© Springer Nature Switzerland AG 2018

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Preface
This volume contains the papers selected for presentation at the 11th Brazilian Sym-
posium on Bioinformatics (BSB 2018), held from October 30 to November 1, 2018, in
Niteroi, Brazil. BSB is an international conference that covers all aspects of bioin-
formatics and computational biology. The event was organized by the Special Interest
Group in Computational Biology of the Brazilian Computer Society (SBC), which has
been the organizer of BSB for the past several years. The BSB series started in 2005. In
the period 2002–2004 its name was Brazilian Workshop on Bioinformatics (WOB).
As in previous editions, BSB 2018 had an international Program Committee (PC) of
31 members. After a rigorous review process by the PC, 13 papers were accepted to be
orally presented at the event, and are published in this volume. All papers were
reviewed by at least three independent reviewers. We believe that this volume repre-
sents a fine contribution to current research in computational biology and bioinfor-
matics, as well as in molecular biology. In addition to the technical presentations, BSB
2018 featured keynote talks from João Meidanis (Universidade Estadual de Campinas),
Peter Stadler (University of Leipzig), and David Sankoff (University of Ottawa).
BSB 2018 was made possible by the dedication and work of many people and
organizations. We would like to express our sincere thanks to all PC members, as well
as to the external reviewers. Their names are listed herein. We are also grateful to the
local organizers and volunteers for their valuable help; the sponsors for making the
event financially viable; and Springer for agreeing to publish this volume. Finally, we
would like to thank all authors for their time and effort in submitting their work and the
invited speakers for having accepted our invitation.
November 2018 Ronnie Alves

Organization
Conference Chairs
Daniel Cardoso de Oliveira Universidade Federal Fluminense, Brazil
Luis Antonio Kowada Universidade Federal Fluminense, Brazil
Ronnie Alves Instituto Tecnológico Vale, Brazil
Local Organizing Committee

André Cunha Ribeiro Instituto Federal de Educação Ciência e Tecnologia,
Brazil
Daniel Cardoso de Oliveira Universidade Federal Fluminense, Brazil
Helene Leitão Universidade Federal Fluminense, Brazil
Luís Felipe Ignácio Cunha Universidade Federal do Rio de Janeiro, Brazil
Simone Dantas Universidade Federal Fluminense, Brazil
Raquel Bravo Universidade Federal Fluminense, Brazil
Program Chair
Steering Committee
Guilherme Pimentel Telles Universidade Estadual de Campinas, Brazil
João Carlos Setubal Universidade de São Paulo, Brazil
Luciana Montera Universidade Federal de Mato Grosso do Sul, Brazil
Maria Emilia Telles Walter Universidade de Brasilia, Brazil
Nalvo Franco de Almeida Jr. Universidade Federal de Mato Grosso do Sul, Brazil
Natália Florencio Martins Empresa Brasileira de Pesquisa Agropecuária, Brazil
Sérgio Vale Aguiar Campos Universidade Federal de Minas Gerais, Brazil
Tainá Raiol Fundação Oswaldo Cruz, Brazil
Program Committee
Alexandre Paschoal Universidade Federal Tecnológica do Paraná, Brazil
André C. P. L. F. de Carvalho Universidade de São Paulo, Brazil
André Kashiwabara Universidade Federal Tecnológica do Paraná, Brazil
Annie Chateau Université de Montpellier, France
César Manuel Vargas Benítez Universidade Federal Tecnológica do Paraná, Brazil
VIII Organization
Fabrício Martins Lopes Universidade Federal Tecnológica do Paraná, Brazil

Felipe Louza Universidade de São Paulo, Brazil
Fernando Luís Barroso Da Universidade de São Paulo, Brazil
Silva
Guilherme Pimentel Telles Universidade Estadual de Campinas, Brazil
Ivan G. Costa RWTH Aachen University, Germany
Jefferson Morais Universidade Federal do Pará, Brazil
Jens Stoye Bielefeld University, Germany
João Carlos Setubal Universidade de São Paulo, Brazil
Kleber Padovani de Souza Universidade Federal do Pará, Brazil
Laurent Bréhélin Université de Montpellier, France
Luciano Antonio Universidade de São Paulo, Brazil
Digiampietri
Luís Felipe Ignácio Cunha Universidade Federal do Rio de Janeiro, Brazil
Marcilio De Souto Université d’Orléans, France
Marcio Dorn Universidade Federal do Rio Grande do Sul, Brazil
Maria Emilia Telles Walter Universidade de Brasilia, Brazil
Mariana Universidade Federal do Rio Grande do Sul, Brazil
Recamonde-Mendoza
Marilia Braga Bielefeld University, Germany
Nalvo Franco de Almeida Jr. Universidade Federal de Mato Grosso do Sul, Brazil
Rommel Ramos Universidade Federal do Pará, Brazil
Said Sadique Adi Universidade Federal de Mato Grosso do Sul, Brazil
Sérgio Vale Aguiar Campos Universidade Federal de Minas Gerais, Brazil
Sergio Lifschitzs Pontifícia Universidade Católica do Rio de Janeiro,
Brazil
Sergio Pantanos Institut Pasteur de Montevideo, Uruguay
Tainá Raiol Fundação Oswaldo Cruz, Brazil
Additional Reviewers
Clement Agret CIRAD, France
Diego P. Rubert Universidade Federal de Mato Grosso do Sul, Brazil
Eloi Araujo Universidade Federal de Mato Grosso do Sul, Brazil
Euler Garcia Universidade de Brasilia, Brazil
Fábio Henrique Viduani Universidade Federal de Mato Grosso do Sul, Brazil
Martinez
Fábio Vicente Universidade Federal Tecnológica do Paraná, Brazil
Francisco Neves Universidade de Brasilia, Brazil
Maria Beatriz Walter Costa Universidade de Brasilia, Brazil
Pedro Feijão Simon Fraser University, Canada
Rodrigo Hausen Universidade Federal do ABC, Brazil
Sèverine Bérard Université de Montpellier, France
Waldeyr Mendes Universidade de Brasilia, Brazil
Organization IX
Sponsors
Sociedade Brasileira de Computação (SBC)

Universidade Federal Fluminense (UFF)
Instituto de Computação, UFF
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Pró-Reitoria de Pesquisa, Pós-graduação e Inovação, UFF
Springer
Contents
Sorting k-Permutations by k-Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Guilherme Henrique Santos Miranda, Alexsandro Oliveira Alexandrino,
Carla Negri Lintzmayer, and Zanoni Dias
Super Short Reversals on Both Gene Order and Intergenic Sizes. . . . . . . . . . 14

Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin,
Ulisses Dias, and Zanoni Dias
Identifying Maximal Perfect Haplotype Blocks . . . . . . . . . . . . . . . . . . . . . . 26

Luís Cunha, Yoan Diekmann, Luis Kowada, and Jens Stoye
Sorting by Weighted Reversals and Transpositions . . . . . . . . . . . . . . . . . . . 38

Andre Rodrigues Oliveira, Klairton Lima Brito, Zanoni Dias,
and Ulisses Dias
Graph Databases in Molecular Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Waldeyr M. C. da Silva, Polyane Wercelens, Maria Emília M. T. Walter,
Maristela Holanda, and Marcelo Brígido
ViMT - Development of a Web-Based Vivarium Management Tool . . . . . . . 58

Cristiano Guimarães Pimenta, Alessandra Conceição Faria-Campos,
Jerônimo Nunes Rocha, Adriana Abalen Martins Dias,
Danielle da Glória de Souza, Carolina Andrade Rezende,
Giselle Marina Diniz Medeiros, and Sérgio Vale Aguiar Campos
An Argumentation Theory-Based Multiagent Model to Annotate Proteins . . . 66

Daniel S. Souza, Waldeyr M. C. Silva, Célia G. Ralha,
and Maria Emília M. T. Walter
AutoModel: A Client-Server Tool for Intuitive and Interactive

Homology Modeling of Protein-Ligand Complexes . . . . . . . . . . . . . . . . . . . 78
João Luiz de A. Filho, Annabell del Real Tamariz,
and Jorge H. Fernandez
Detecting Acute Lymphoblastic Leukemia in down Syndrome Patients

Using Convolutional Neural Networks on Preprocessed Mutated Datasets . . . 90
Maram Shouman, Nahla Belal, and Yasser El Sonbaty
S2 FS: Single Score Feature Selection Applied to the Problem of

Distinguishing Long Non-coding RNAs from Protein Coding Transcripts. . . . 103
Bruno C. Kümmel, Andre C. P. L. F. de Carvalho, Marcelo M. Brigido,
Célia G. Ralha, and Maria Emilia M. T. Walter
XII Contents
A Genetic Algorithm for Character State Live Phylogeny. . . . . . . . . . . . . . . 114

Rafael L. Fernandes, Rogério Güths, Guilherme P. Telles,
Nalvo F. Almeida, and Maria Emília M. T. Walter
A Workflow for Predicting MicroRNAs Targets via Accessibility

in Flavivirus Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Andressa Valadares, Maria Emília Walter, and Tainá Raiol
Parallel Solution Based on Collective Communication Operations

for Phylogenetic Bootstrapping in PhyML 3.0 . . . . . . . . . . . . . . . . . . . . . . 133
Martha Torres and Julio Oliveira da Silva
Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

Sorting λ-Permutations by λ-Operations
Guilherme Henrique Santos Miranda1(B) ,

Alexsandro Oliveira Alexandrino1 , Carla Negri Lintzmayer2 ,
and Zanoni Dias1
1
Institute of Computing, University of Campinas (Unicamp), Campinas, Brazil
{guilherme.miranda,alexsandro.alexandrino}@students.ic.unicamp.br,
zanoni@ic.unicamp.br
2
Center for Mathematics, Computation and Cognition,
Federal University of ABC (UFABC), Santo André, Brazil
carla.negri@ufabc.edu.br
Abstract. The understanding of how different two organisms are is one

of the challenging tasks of modern science. A well accepted way to esti-
mate the evolutionary distance between two organisms is estimating the
rearrangement distance, which is the smallest number of rearrangements
needed to transform one genome into another. If we represent genomes
as permutations, we can represent one as the identity permutation and
so we reduce the problem of transforming one permutation into another
to the problem of sorting a permutation using the minimum number of
operations. In this work, we study the problems of sorting permutations
using reversals and/or transpositions, with some additional restrictions
of biological relevance. Given a value λ, the problem now is how to sort a
λ-permutation, which is a permutation where all elements are less than λ
positions away from their correct places (regarding the identity), by apply-
ing the minimum number of operations. Each λ-operation must have size
at most λ and, when applied over a λ-permutation, the result should also
be a λ-permutation. We present algorithms with approximation factors
of O(λ2 ), O(λ), and O(1) for the problems of Sorting λ-Permutations by
λ-Reversals, by λ-Transpositions and by both operations.
Keywords: Genome rearrangements · Approximation algorithms

Sorting permutations
1 Introduction
One challenge of modern science is to understand how species evolve, considering
that new organisms arise from mutations that occurred in others. Using the
principle of parsimony, the minimum number of rearrangements that transform
one genome into another, called rearrangement distance, is considered a well
accepted way to estimate the evolutionary distance between two genomes. A
genome rearrangement is a global mutation that alters the order and/or the
orientation of the genes in a genome.
c Springer Nature Switzerland AG 2018
R. Alves (Ed.): BSB 2018, LNBI 11228, pp. 1–13, 2018.
https://doi.org/10.1007/978-3-030-01722-4_1
2 G. H. S. Miranda et al.
Depending on the genomic information available and the problems consid-

ered, a genome can be modeled in different ways. Considering that a genome
has no repeated genes, we can model it as a permutation, with each element rep-
resenting a gene or a genomic segment shared by the genomes being compared.
If the information about orientation is available, we use signed permutations
to represent them. When this information is unknown, we simply use unsigned
permutations. In this work, we only deal with the case where the orientation is
unknown. By representing one of the genomes as the identity permutation, we
reduce the problem of transforming one permutation into another to the problem
of sorting a permutation with the minimum number of rearrangements, which is
called sorting rearrangement distance or simply distance.
A rearrangement model M is the set of valid rearrangements used to calcu-
late the distance. A reversal rearrangement inverts a segment of the genome
and a transposition rearrangement swaps two adjacent segments of the genome.
Genome rearrangements are also sometimes called operations.
The problems of Sorting Permutations by Reversals and Sorting Permuta-
tions by Transpositions are NP-Hard [2,3]. The best-known results for both
problems are approximation algorithms with factor 1.375 [1,6]. Walter et al. [13]
considered a variation in which the rearrangement model contains both rever-
sals and transpositions, which is called Sorting Permutations by Reversals and
Transpositions, and they presented a 3-approximation algorithm for it. However,
the best-known approximation factor for this problem is 2k [11], where k is
the approximation factor of an algorithm used for cycle decomposition of the
breakpoint graph [5]. Given the best-known value for k, this algorithm has an
approximation factor of 2.8386 + , where > 0. The complexity of this problem
is still unknown.
Many variants of the sorting rearrangement distance emerged from the
assumption that rearrangement operations which affect large portions of a
genome are less likely to occur [9]. Most of these variants add a constraint that
limits the size of a valid operation [7,8,12]. Considering a size-limit of 2, the prob-
lems of Sorting Permutations by Reversals and/or Transpositions are solvable
in polynomial time [7]. Considering a size-limit of 3, the best-known approxima-
tion factors for Sorting Permutations by Reversals, by Transpositions, and by
Reversals and Transpositions are 2 [7], 5/4 [8], and 2 [12], respectively.
The problem of Sorting Permutations by λ-operations is a generalization of
the size-limited variants in which a rearrangement operation is valid if its size is
less than or equal to λ. Miranda et al. [10] presented O(λ2 )-approximation algo-
rithms for reversals, transpositions, and both operations. Using size-limited oper-
ations makes more sense when one knows that the elements are not so far away
from their original positions, so we introduce the study of Sorting λ-Permutations
by λ-Operations. A permutation π is a λ-permutation if all elements of π are
at a distance less than λ from their correct positions considering the identity
permutation. We will consider the problems of sorting unsigned λ-permutations
by λ-reversals, by λ-transpositions, and by λ-reversals and λ-transpositions.
Sorting λ-Permutations by λ-Operations 3
Next sections are organized as follows. In Sect. 2, we present all the concepts
used in this paper. In Sect. 3, we present O(λ2 )-approximation algorithms for the
problems studied. In Sect. 4, we present algorithms with approximation factors
of O(λ) and O(1). In Sect. 5, we show experimental results which compare the
algorithms presented in Sects. 3 and 4. We conclude the paper in Sect. 6.
2 Definitions
We denote a permutation by π = (π1 π2 . . . πn ), where πi ∈ {1, 2, . . . , n} and
πi = πj , for all 1 ≤ i < j ≤ n. We assume that there are two extra elements
π0 = 0 and πn+1 = n + 1 in π, but, for convenience, they are omitted from the
permutation’s representation. Given an integer λ as input, we say that π is a
λ-permutation if we have |πi − i| < λ for all 1 ≤ i ≤ n.
We denote the inverse permutation of π as π −1 . This permutation is such
that ππ−1
i
= i for all 1 ≤ i ≤ n. Note that element πi−1 indicates the position of
element i in π. For example, given π = (4 6 3 5 2 1), then π −1 = (6 5 3 1 4 2).
An operation of reversal is denoted by ρ(i, j), with 1 ≤ i < j ≤ n, and when
applied on a permutation π = (π1 π2 . . . πn ), the result is permutation π · ρ(i, j)
= (π1 π2 . . . πi−1 πj πj−1 . . . πi+1 πi πj+1 . . . πn−1 πn ). The size of a reversal
is given by j − i + 1. For example, given π = (1 4 3 2 5), then π · ρ(2, 4) = (1 2
3 4 5) and the size of such operation is 4 − 2 + 1 = 3. We say that ρ(i, j) is a
λ-reversal if we have j − i + 1 ≤ λ.
An operation of transposition is denoted by τ (i, j, k), with 1 ≤ i < j < k
≤ n + 1, and when applied on a permutation π = (π1 π2 . . . πn ), the result is
permutation π · τ (i, j, k) = (π1 π2 . . . πi−1 πj . . . πk−1 πi . . . πj−1 πk . . . πn ).
The size of a transposition is given by k − i. For example, given π = (4 5 6 1 2
3), then π · τ (1, 4, 7) = (1 2 3 4 5 6) and the size of such operation is 7 − 1 = 6.
We say that τ (i, j, k) is a λ-transposition if we have k − i ≤ λ.
The goal of these problems is to transform a λ-permutation π into the identity
permutation ι = (1 2 . . . n) by applying the minimum number of λ-operations,
which defines the sorting distance, such that each permutation generated during
the process is also a λ-permutation.
We denote by dλr (π), dλt (π), and dλrt (π), the sorting distance when we have
only λ-reversals, only λ-transpositions, and when we have both operations,
respectively.
3 Inversions-Based Approximation Algorithms

In this section we present approximation algorithms based on the concept of
inversions for the problems we are addressing.
An inversion is defined as a pair of elements (πi , πj ) such that i < j and
πi > πj . The number of inversions in π is denoted by Inv(π).
Lemma 1. For all λ-permutations π = ι and all λ ≥ 2, we have dλr (π) ≥
Inv(π) λ Inv(π) λ Inv(π)
λ(λ−1)/2 , dt (π) ≥ λ(λ−1)/2 , and drt (π) ≥ λ(λ−1)/2 .
Proof. This follows immediately from the observation that a λ-reversal and a
λ-transposition can remove at most λ(λ−1)
2 inversions.

Next lemma shows that it is always possible to remove at least one inver-
sion from a λ-permutation by applying one λ-operation which results in a λ-
permutation.
Lemma 2. Let π be a λ-permutation. It is always possible to obtain a λ-

permutation with Inv(π) − 1 inversions by applying one λ-reversal or one λ-
transposition.
Proof. Let πj = i be the smallest element out-of-place (πi = i) in π. Initially,

note we have inversion (πj−1 , πj ), since πj−1 > πj and j − 1 < j. Let σ be a
λ-operation that swaps elements πj−1 and πj , and let π = π · σ. It is easy to
see that Inv(π ) = Inv(π) − 1, since such inversion was removed, and note that
there always exists a λ-reversal or a λ-transposition equivalent to σ, because the
elements are adjacent and so both only swap two elements.
Observe that, in π , element πj is closer to its correct position, since it was
moved to the left. Hence, we follow by showing that π is a λ-permutation by
considering two cases according to the values of πj−1 = πj .
If πj−1 ≥ j, then πj−1 is also closer to its correct position, in π . Otherwise,
πj−1 < j. Thus, element πj−1 will be, in π , one position away from its correct
position. Then, note that |j − πj | + 1 = (j − i) + 1 ≤ λ, because π is a λ-
permutation. Also observe that we have |j − πj | = j − πj because πj = πj−1 < j,
and j − πj < j − i because πj > i, and, so, j − i ≤ λ − 1. Therefore, π is a
λ-permutation and the result follows.

A generic greedy approximation algorithm for the three problems we are

addressing is presented in next theorem. It receives an integer λ ≥ 2 and a λ-
permutation π = ι as inputs. It is greedy because it always tries to decrease the
largest amount of inversions in π. Since the only permutation with no inversions
is the identity, it will, eventually, sort π.
Theorem 3. There exist O(λ2 )-approximation algorithms for the problems of

Sorting λ-Permutations by λ-Reversals, λ-Transpositions, and by λ-Reversals
and λ-Transpositions.
Proof. Let λ ≥ 2 be an integer and let π = ι be a λ-permutation. Consider an

algorithm which chooses the λ-operation σ such that π · σ is a λ-permutation
and Inv(π · σ) is as small as possible and then it applies such operation over
π. The algorithm repeats the same process in the resulting permutation until it
reaches the identity permutation.
In the worst case, we always have one λ-operation reducing the number of
inversions by one unit, as shown in Lemma 2. Therefore, the number of opera-
tions of such greedy algorithm is at most Inv(π), and the approximation factor
follows immediately from Lemma 1.

Note that the distance is O(n2 ) because any permutation can be sorted with
O(n2 ) λ-reversals or λ-transpositions. For Sorting by λ-Reversals, at each step
the algorithm considers O(λ2 ) possible reversals that can be chosen. Since the
variation
√ in the number of inversions caused by an operation can be calculated
√
in O(λ log λ) time [4], the algorithm has total time complexity O(n2 λ3 log λ).
Using the same analysis, we conclude that √ the algorithms involving transposi-
tions have total time complexity O(n2 λ4 log λ).
4 Breakpoints-Based Approximation Algorithms
In this section we present approximation algorithms based on the concept of

breakpoints for the three problems we are addressing.
A breakpoint is defined as a pair of elements (πi , πi+1 ) such that πi+1 − πi =
1 (resp. |πi+1 − πi | = 1), for all 0 ≤ i ≤ n, in the problems of Sorting λ-
Permutations by λ-Transpositions (resp. Sorting λ-Permutations by λ-Reversals
and Sorting λ-Permutations by λ-Reversals and λ-Transpositions). The number
of breakpoints in π is denoted by b(π).
b(π)
Lemma 4. For all λ-permutations π = ι and all λ ≥ 2 we have dλr (π) ≥ 2 ,
dλt (π) ≥ b(π) λ b(π)
3 , and drt (π) ≥ 3 .
Proof. This follows immediately from the observation that a λ-reversal and a
λ-transposition can remove at most 2 and 3 breakpoints, respectively.

A maximal subsequence (πi πi+1 . . . πj ) without any breakpoints (πk , πk+1 ),

for all i ≤ k < j, is called a strip. If the strip’s elements are in ascending (resp.
descending) order, then we call it an increasing (resp. decreasing) strip. Strips
containing only one element are considered to be increasing. For example, con-
sidering sorting by both operations and π = (6 4 5 3 2 1), we have two increasing
strips (6) and (4 5), and a decreasing strip (3 2 1). Note, however, that segment
(3 2 1) is not a decreasing strip for the problem of Sorting by Transpositions.
This is because, direct from the definition of strips and breakpoints, there are
no decreasing strips when this problem is considered. The number of elements
in a strip S of a λ-permutation π is denoted by |S|.
Lemma 5. Let π be a λ-permutation and let πj = i be the smallest element

out-of-place in π. The strip S that contains πj is such that |S| ≤ λ − 1.
Proof. First, suppose we have S = (πj . . . πk ) as an increasing strip. Then,

let R = (πi . . . πj−1 ) be the segment of elements to the left of S. Note that
any element in R is greater than any element in S and, so, πi ≥ k + 1, since
πi > πk . By contradiction, suppose |S| ≥ λ. Then, we have i ≤ k − λ + 1. Since
i ≤ (k + 1) − λ ≤ k + 1 ≤ πi , we also have that i ≤ πi , and so |πi − i| = πi − i ≥
k + 1 − (k + 1 − λ) = λ > λ − 1, which is a contradiction to the definition of
λ-permutations. When we have πj in a decreasing strip, the proof follows by
symmetry.

In next lemma, we suppose that the smallest element out-of-place is in an

increasing strip of a λ-permutation π = ι and we show how to reduce the number
of breakpoints of π by moving this strip to its correct position, but without
considering λ-operations. It is auxiliar to Lemmas 7 and 8, which show how to
do this by applying a sequence of λ-transpositions. Lemma 9 shows how to do
this when the smallest element out-of-place is in a decreasing strip.
Lemma 6. Let π be a λ-permutation. Let πj = i be the smallest element out-

of-place in π. Suppose that πj is in an increasing strip S = (πj . . . πk ). Then
b(π · τ (i, j, k + 1)) ≤ b(π) − 1 and (k + 1 − i) ≤ 2(λ − 1).
Proof. Let R = (πi . . . πj−1 ) be the segment of elements in π that will be trans-
posed with S. Observe that any element in R is greater than any element in S,
so π · τ (i, j, k + 1) is a λ-permutation, once greater elements are moved to the
right and smaller elements to the left. Also observe that in π we have the three
breakpoints (πi−1 , πi ), (πj , πj+1 ), and (πk−1 , πk ), where the first one is because
πi−1 = πj − 1 = i − 1 and πi > i = πj and the second and third ones are because
the strip’s start and strip’s end are at positions j and k, respectively. Transposi-
tion τ (i, j, k+1) moves the elements of S to their correct positions by transposing
them with elements of R, thus removing at least breakpoint (πi−1 , πi ). Since a
transposition can add at most three breakpoints, but we already had all of them
and we removed at least (πi−1 , πi ), we have b(π · τ (i, j, k + 1)) ≤ b(π) − 1.
By Lemma 5, we have |S| ≤ λ − 1, thus k + 1 − j ≤ λ − 1. Since π is a
λ-permutation, we have |πj − j| ≤ λ − 1, and, by construction, πj = i, thus
|i − j| + 1 = j − i + 1 ≤ λ − 1. Therefore, k + 1 − i ≤ 2(λ − 1).

Lemma 7. Let π be a λ-permutation. Let πj = i be the smallest element out-

of-place in π. Suppose that π only has increasing strips and that πj is in a strip
S = (πj . . . πk ). It is always possible to obtain a λ-permutation π · τ (i, j, k + 1)
with at most b(π) − 1 breakpoints by applying at most 5 + (λ − 1)/2 λ-reversals
such that all intermediary permutations are λ-permutations.
Proof. Let R = (πi . . . πj−1 ) be the segment that will be moved to the right in
τ (i, j, k + 1). Note that |S| ≤ λ − 1, by Lemma 5, and |R| ≤ λ − 1, because π is
a λ-permutation.
The idea is to move elements from S to their correct positions by applying at
most two sequences of pairs of λ-reversals, where each one puts at most λ/2
elements of S in their correct positions at a time.
In the first sequence of λ-reversals, there are two possibilities. If |S| ≤ λ/2 ,
then the first operation of each pair reverts |S| elements contained in both S
and R. If |S| > λ/2 , then it reverts λ/2 elements contained in both S and
R. In any case, the second operation of each pair reverts back the elements of
R affected by the first one, in order to leave π with only increasing strips again
(except for the elements of S which were affected by the first operation).
After the sequence is applied, we have at most λ/2 elements of S from
positions i to i + min( λ/2 , |S|), and, maybe, they are in a decreasing strip. If
this is the case, then one more λ-reversal has to be applied to put these elements
in their correct places, by reversing such decreasing strip.
The second sequence of λ-reversals puts the at most λ/2 remaining elements
of S in their correct positions, following the same idea, and, also, maybe one
extra λ-reversal will be necessary after it is applied. Note that, if there are no
remaining elements (in case of |S| ≤ λ/2 ), this sequence is not necessary.
The largest amount of operations needed in the process described above
happens when we have exactly λ/2 + 1 elements in S. In order to put the first
λ/2 elements of S in their correct positions, in this case, we have to apply at
most (λ − 1)/( (λ/2) + 1) pairs of λ-reversals and, maybe, one extra at the
end. Since each pair of operations puts λ/2 elements exactly (except, maybe,
by the last pair) λ/2 + 1 positions to the left, the number of operations needed
is 4 + 1 = 5. Then, to move the remaining element of S to its correct position,
all the λ-reversals of the second sequence will have size 2 (note that, in this case,
we do not need the second operation of each pair), which means such element
will be moved only 2 positions to the left per operation, giving an extra amount
of (λ − 1)/2 λ-reversals. Therefore, the number of λ-reversals to move S to its
correct position is at most 5 + (λ − 1)/2 λ-reversals.
Now we have to show that after each operation is applied, we have a λ-
permutation as result and, after the last operation is applied, we have π·τ (i, j, k+
1). Observe that any element in R is greater than any element in S. Then, once
the first operation of each pair moves elements of R to the right and elements
of S to the left, all elements affected will be closer to their correct positions,
resulting in a λ-permutation. The second operation of each pair reverts elements
of R to ascending order again, so it also results in a λ-permutation. After both
sequences of λ-reversals are applied, all elements of S are at positions from i to
i + k − j and all elements of R are at positions from i + k − 1 to k, resulting in
π · τ (i, j, k + 1), which is a λ-permutation with at least one less breakpoint than
π, as showed in Lemma 6.

Lemma 8. Let π be a λ-permutation. Let πj = i be the smallest element out-of-

place in π. Suppose that πj is in an increasing strip S = (πj . . . πk ). It is always
possible to obtain a λ-permutation π · τ (i, j, k + 1) with at most b(π) − 1 reversal
breakpoints by applying at most 4 λ-transpositions such that all intermediary
permutations are λ-permutations.
Proof. Let R = (πi . . . πj−1 ) be the segment that will be moved to the right in
τ (i, j, k + 1). Note that |S| ≤ λ − 1, by Lemma 5, and |R| ≤ λ − 1, because π is
a λ-permutation.
The idea is to apply a sequence with at most four λ-transpositions that divide
both segments R = (πi . . . πj−1 ) and S = (πj . . . πk ) into at most two parts
each, where each part has at most λ/2 elements, and then exchange each part
of S at most twice (and at least once), with the (possible) two parts of R. If
we had exactly λ − 1 elements in each of S and R, such sequence would be
τ (i + λ/2 , j, j + λ/2 ), τ (i, i + λ/2 , j), τ (j, j + λ/2 , k + 1), τ (i + λ/2 , j, j +
λ/2 ).
Now we have to show that after each of the at most four operations is applied,
we have a λ-permutation as result. Observe that any element in R is greater
than any element in S. Since each λ-transposition puts elements of S closer to
their correct positions by transposing them with greater elements of R, we have
a λ-permutation after each λ-operation applied. After all λ-transpositions are
applied, the elements of S are at positions from i to i + k − j and the elements
of R are at positions from i + k − j + 1 to k, resulting in π · τ (i, j, k + 1), which
is a λ-permutation with at least b(π) − 1 breakpoints, as showed in Lemma 6.
Lemma 9. Let πk = i be the smallest element out-of-place in a λ-permutation

π. Suppose that πk is in a decreasing strip S = (πj . . . πk ). It is always possible
to obtain a λ-permutation with at most b(π) − 1 reversal breakpoints by applying
at most one λ-transposition and one λ-reversal.
Proof. When j = i, one reversal ρ(j, k) put elements of S in their correct posi-
tions. Since |S| = k − j + 1 ≤ λ − 1 by Lemma 5, we have ρ(j, k) is a λ-reversal
and, since such operation just reverts a decreasing strip, we also have π · ρ(j, k)
as a λ-permutation.
Now assume j > i. Note that, in this case, we have the three breakpoints
(πi−1 , πi ), (πj , πj+1 ), and (πk−1 , πk ), where the first one is because πi−1 = πk −
1 = i − 1 and πi > i = πk and the second and third ones are because the strip’s
start and strip’s end are at positions k and j, respectively. Thus, we can apply
the λ-transposition τ (i, j, k + 1) followed by the λ-reversal ρ(i, i + (k − j)) and
then we get b(π · τ (i, j, k + 1) · ρ(i, i + (k − j))) ≤ b(π) − 1, once a λ-transposition
can add at most three breakpoints but we already had (πi−1 , πi ), (πj−1 , πj ),
and (πk , πk+1 ), and the second λ-reversal can add at most two breakpoints but
we already had (πi−1 , πj ) and (πk , πi ) and we removed the first one, since all
elements of S will be in their correct positions in π · τ (i, j, k + 1) · ρ(i, i + (k − j)).
Now we have to show that after each operation is applied, we have a λ-
permutation as result. Let R = (πi . . . πj−1 ) be the segment of elements that
should be moved in order to put S in its correct position. Observe that any ele-
ment in R is greater than any element in S. The first operation, a λ-transposition,
transposes S only with greater elements and thus the result is a λ-permutation.
The second operation, a λ-reversal, just reverts a decreasing strip to put the
elements of S in their correct positions, thus it also results in a λ-permutation.
Hence, we have as result a λ-permutation with at least one less breakpoint.
Next theorems describe approximation algorithms for the problems we are

addressing. Lemma 10 is auxiliar to Theorem 11. The algorithms receive an
integer λ ≥ 2 and a λ-permutation π = ι as input. The goal is to decrease at
least one unit on the number of breakpoints in π by moving elements to their
correct positions (applying Lemmas 8 and 9). Since the only permutation with
no breakpoints is the identity, they will, eventually, sort π.
Lemma 10. Let π be a λ-permutation. Let S = (j . . . i) be a decreasing strip

in π (thus i < j). Let π = π · ρ(πj−1 , πi−1 ) be the resulting permutation after
reverting S in π. Then, π is a λ-permutation.
Proof. First note that element πj is to the right of element πi . We show that the
lemma follows by considering four cases, according to the positions of elements
i and j with relation to the elements πi and πj .
Case (i), i < j < πj−1 < πi−1 : note that both πi and πj are to the left of S.
Then, after reverting S, element i is closer to its correct position, while element
j is moved away from its correct position. Despite this, the distance between πj
and j in π is smaller than the distance between πi and i in π, and so if π is a
λ-permutation, π is also a λ-permutation.
Case (ii), i < πj−1 ≤ j < πi−1 : note that πi is to the left of S and πj is in
S. Then, after reverting S, the element i is closer to its correct position and the
distance of j to its correct position will still be less than λ, since the size of S is
at most λ, as Lemma 5 shows.
Case (iii), πj−1 ≤ i < πi−1 ≤ j: similar to (ii).
Case (iv), πj−1 < πi−1 ≤ i < j: similar to (i).

Theorem 11. The problem of Sorting λ-Permutations by λ-Reversals has a

O(λ)-approximation algorithm.
Proof. Let λ ≥ 2 be an integer and π = ι be a λ-permutation. Consider an

algorithm which first applies one λ-reversal over each decreasing strip of π in
order to get a λ-permutation with only increasing strips. By Lemma 10, we
guarantee that all intermediary permutations generated by these λ-reversals are
λ-permutations.
Then, the algorithm will repeatedly take the smallest element out-of-place
and move the increasing strip that contains it to its correct position, obtaining
a λ-permutation with at least one less breakpoint, until it reaches the identity
permutation.
As shown in Lemma 7, at most 5+ (λ−1)/2 λ-reversals are needed to move
each strip to its correct position. Since, maybe, one extra λ-reversal could have
been applied in the beginning of the algorithm to transform such strip into an
increasing one, we have that at most 6 + (λ − 1)/2 λ-reversals can be applied
to remove at least one breakpoint. Therefore, the number of operations of our
algorithm is at most (6 + (λ − 1)/2 )b(π) ≤ O(λ)dλr (π), where the inequality
follows from Lemma 4.

Theorem 12. The problem of Sorting λ-Permutations by λ-Transpositions has

a 12-approximation algorithm.
Proof. Let λ ≥ 2 be an integer and let π = ι be a λ-permutation. The algo-

rithm will repeatedly take the smallest element out-of-place and move the
increasing strip that contains such element to its correct position, obtaining
a λ-permutation with at least one less breakpoint, until it reaches the identity
permutation.
As shown in Lemma 8, at most 4 λ-transpositions are needed to move each
strip to its correct position. Then, in the worst case, we remove 1 breakpoint
every 4 λ-transpositions applied. With this and Lemma 4, the number of opera-
tions of our algorithm is at most 4b(π) ≤ 12dλt (π).

Theorem 13. The problem of Sorting λ-Permutations by λ-Reversals and λ-

Transpositions has a 12-approximation algorithm.
Proof. Let λ ≥ 2 be an integer and let π = ι be a λ-permutation. Let πj = i

be the smallest element out-of-place in π. We have two cases to consider: when
the strip which contains πj is decreasing or not. In both cases, we can at least
remove breakpoint (πi−1 , πi ) from π without adding other ones by applying at
most 4 λ-transpositions (if the strip is increasing) or at most 2 λ-operations (if
the strip is decreasing), as showed in Lemmas 8 and 9, respectively.
Then, considering both cases described, the algorithm will repeatedly take
the smallest element out-of-place and move the strip that contains it to its correct
position, decreasing at least one breakpoint at a time, until it reaches the identity
permutation.
Note that, in the worst case, we remove 1 breakpoint every 4 λ-transpositions
and so the result is analogous to Theorem 12.

Since b(n) ≤ n + 1, the algorithms move the strip containing the smallest ele-
ment out of place at most O(n) times. At each step, the algorithms spend O(n)
time to find the strip to move and they spend O(λ) (O(1)-approximation algo-
rithms) or O(λ2 ) (O(λ)-approximation algorithms) time to apply the operations
to move such strip. So, the time complexity for the O(1)-approximation algo-
rithms and the O(λ)-approximation algorithm are O(n(n+λ)) and O(n(n+λ2 )),
respectively.
5 Experimental Results
We have implemented the inversions-based and the breakpoints-based approxi-

mation algorithms in order to analyze how they work in a practical perspective.
We performed experiments considering a total of 1000 random λ-permutations,
with size equal to 100 and values of λ = 5, 10, 15, . . . , 100, as input for the algo-
rithms. Then, we compared the results according to the average and maximum
approximation factors obtained for all permutations. For each permutation, we
considered the maximum value of lower bound between the ones shown in Lem-
mas 1 and 4.
We show the results in Fig. 1. We observed that the maximum approximation
factors were 5.38 and 6.76 for λ-reversals, 2.91 and 3.15 for λ-transpositions, and
3.00 and 3.18 for when both operations are allowed, considering the breakpoints-
based and the inversions-based algorithm, respectively. We also noticed, in our
tests, the average approximation factor of the inversions-based algorithm and
the breakpoints-based algorithm were similar, even with the relevant difference
among their theoretical approximation factors.
7.0
6.0
Approximation Factor
5.0
4.0
3.0
2.0
Inversions-based Approximation Algorithm (Average)
Inversions-based Approximation Algorithm (Maximum)
1.0 Breakpoints-based Approximation Algorithm (Average)
Breakpoints-based Approximation Algorithm (Maximum)
0.0
0 10 20 30 40 50 60 70 80 90 100
λ
(a) Sorting λ-Permutations by λ-Reversals.
3.5
3.0
2.5
2.0
1.5
1.0
0.0
0 10 20 30 40 50 60 70 80 90 100
λ
(b) Sorting λ-Permutations by λ-Transpositions.
3.5
3.0
2.5
2.0
1.5
1.0
0.0
0 10 20 30 40 50 60 70 80 90 100
λ
(c) Sorting λ-Permutations by λ-Reversals and λ-Transpositions.
Fig. 1. Average and maximum approximation factors of the algorithms for Sorting
λ-Permutations by λ-Operations, with λ-permutations of size 100.
6 Conclusion
In this work we introduced the study of the problems of Sorting λ-Permutations
by λ-Operations. We developed algorithms with approximation factors of O(λ2 ),
O(λ), and 12 for the problems studied. We also performed experiments in order to
compare how the algorithms work in a practical perspective. For future work, we
intend to develop approximation algorithms for the problems of Sorting Signed
λ-Permutations by λ-Operations.
Acknowledgments. This work was supported by the Brazilian Federal Agency for the
Support and Evaluation of Graduate Education, CAPES, the National Counsel of Tech-
nological and Scientific Development, CNPq (grants 400487/2016-0 and 425340/2016-
3), São Paulo Research Foundation, FAPESP (grants 2013/08293-7, 2015/11937-9,
2017/12646-3, 2017/16246-0, and 2017/16871-1), and the program between the CAPES
and the French Committee for the Evaluation of Academic and Scientific Cooperation
with Brazil, COFECUB (grant 831/15).
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Super Short Reversals on Both Gene
Order and Intergenic Sizes
Andre Rodrigues Oliveira1(B) , Géraldine Jean2 , Guillaume Fertin2 ,

Ulisses Dias3 , and Zanoni Dias1
1
Institute of Computing, University of Campinas, Campinas, Brazil
{andrero,zanoni}@ic.unicamp.br
2
Laboratoire des Sciences du Numérique de Nantes, UMR CNRS 6004,
University of Nantes, Nantes, France
{geraldine.jean,guillaume.fertin}@univ-nantes.fr
3
School of Technology, University of Campinas, Limeira, Brazil
ulisses@ft.unicamp.br
Abstract. The evolutionary distance between two genomes can be esti-

mated by computing the minimum length sequence of operations, called
genome rearrangements, that transform one genome into another. Usu-
ally, a genome is modeled as an ordered sequence of (possibly signed)
genes, and almost all the studies that have been undertaken in the
genome rearrangement literature consist in shaping biological scenarios
into mathematical models: for instance, allowing different genome rear-
rangements operations at the same time, adding constraints to these rear-
rangements (e.g., each rearrangement can affect at most a given number
k of genes), considering that a rearrangement implies a cost depending
on its length rather than a unit cost, etc. However, most of the works
in the field have overlooked some important features inside genomes,
such as the presence of sequences of nucleotides between genes, called
intergenic regions. In this work, we investigate the problem of comput-
ing the distance between two genomes, taking into account both gene
order and intergenic sizes; the genome rearrangement operation we con-
sider here is a constrained type of reversals, called super short reversals,
which affect up to two (consecutive) genes. We propose here three algo-
rithms to solve the problem: a 3-approximation algorithm that applies to
any instance, and two additional algorithms that apply only on specific
types of genomes with respect to their gene order: the first one is an
exact algorithm, while the second is a 2-approximation algorithm.
Keywords: Genome rearrangements · Intergenic regions

Super short reversals · Approximation algorithm
1 Introduction
Given two genomes G1 and G2 , one way to estimate their evolutionary distance
is to compute the minimum possible number of large scale events, called genome
c Springer Nature Switzerland AG 2018
R. Alves (Ed.): BSB 2018, LNBI 11228, pp. 14–25, 2018.
https://doi.org/10.1007/978-3-030-01722-4_2
Super Short Reversals on Both Gene Order and Intergenic Sizes 15
rearrangements, that are needed to go from G1 to G2 . The minimality requirement

is dictated by the commonly accepted parsimony principle, while the allowed
genome rearrangements depend on the model, i.e. on the classes of events that
supposedly happen during evolution.
However, before one performs this task, it is necessary to model the input
genomes. Almost all previous works have defined genomes as ordered sequences
of elements, which are genes. Variants within this setting can occur: for instance,
depending on the model, genes may be signed or unsigned, the sign of a gene
representing the DNA strand it lies on. Besides, each gene may appear either
once or several times in a genome: in the latter case, genomes are modeled as
strings, while in the former case they are modeled as permutations.
Concerning genome rearrangements, the most commonly studied is reversal,
which consists in taking a continuous sequence in the genome, reversing it, and
putting it back at the same location (see e.g. [10] for one of the first studies
of the problem). A more recent and general type of genome rearrangement is
the DCJ (for Double-Cut and Join) [14]. One can also alternately define the
rearrangement events in order to reflect specific biological scenarios. For example,
in populations where the number of rearrangement events that affect a very large
portion of the genes is known to be rare, we can restrict events to be applied
over no more than k genes at the same time, for some predetermined value of
k [5,8,9].
Since the mid-nineties, a very large amount of work has been done concerning
algorithmic issues of computing distances between pairs of genomes, depending
on the genome model and the allowed set of rearrangements. For instance, if
one considers reversals in unsigned permutations, the problem is known to be
NP-hard [4], while it is polynomial-time solvable in signed permutations [10].
We refer the reader to Fertin et al.’s book [7] for a survey of the algorithmics
aspects of the subject.
As previously mentioned, almost all of these works have so far assumed that
a genome is an ordered sequence of genes. However, it has recently been argued
that this model could underestimate the “true” evolutionary distance, and that
other genome features may require to be taken into account in the model in
order to circumvent this problem [1,2].
Indeed, genomes carry more information than just their ordered sequences of
genes, and in particular consecutive genes in a genome are separated by inter-
genic regions, which are DNA sequences between genes having different sizes (in
terms of number of nucleotides).
This recently led some authors to model a genome as an ordered sequence of
genes, together with an ordered list of its intergenic sizes, and to consider the
problem of computing the DCJ distance, either in the case where insertions and
deletions of nucleotides are forbidden [6], or allowed [3].
In this work, we also consider genomes as ordered sequences of genes together
with their intergenic sizes, in the case where the gene sequence is an unsigned
permutation and where the considered rearrangement operation is super short
reversal (or SSR, i.e. a reversal of (gene) length at most two). In this context, our
16 A. R. Oliveira et al.
goal is to determine the minimum number of SSRs that transform one genome
into another.
Sorting by super short reversals and/or super short transpositions (i.e. trans-
positions of (gene) length at most two each) has been studied in linear and circu-
lar genomes, signed and unsigned, and in all cases the problem has been shown
to be in P class [8,9,11–13].
This paper is organized as follows. In Sect. 2 we provide the notations that
we will use throughout the paper, and we introduce new notions that will prove
useful for studying the problem. In Sect. 3, we derive lower and upper bounds on
the sought distance, which in turn will help us design three different algorithms:
one applies to the general case, while the remaining two apply to specific classes
of genomes. Section 4 concludes the paper.
2 Definitions
We can represent a genome G with n genes as an n-tuple. When there is no
duplicated genes, the n-tuple is a permutation π = (π1 π2 ... πn−1 πn ) with
πi ∈ {1, 2, ..., (n−1), n}, for 1 ≤ i ≤ n, and πi = πj if, and only if, i = j. We
denote by ι the identity permutation, the permutation in which all elements are
in ascending order. The extended permutation is obtained from π by adding two
new elements: π0 = 0 and πn+1 = (n+1).
A genome G, represented by a permutation π with n elements, has m = n + 1
intergenic regions rπ = (r1π , ..., rm π
), with rjπ ≥ 0 for 1 ≤ j ≤ m, such that
the intergenic region ri is located before element πi , for 1 ≤ i ≤ n, and the
π
π
intergenic region rm is situated right after element πn .
A reversal ρ(i, j, x, y) applied over a permutation π, with 1 ≤ i ≤ j ≤ n,
0 ≤ x ≤ riπ , and 0 ≤ y ≤ rj+1 π
, is an operation that (i) reverses the order of the
elements in the subset of adjacent elements {πi , ..., πj }; (ii) reverses the order
of intergenic regions in the subset of adjacent intergenic regions {ri+1 π
, ..., rjπ }
when j > i + 2; (iii) cuts two intergenic regions: after position x inside intergenic
region riπ and after position y inside intergenic region rj+1 π
. This reversal results

in the permutation π such that ri = x + y and rj+1 = (riπ −x) + (rj+1
π π π
−y).
A reversal ρ(i, j, x, y) is also called a k-reversal, where k = (j −i)+1. A super
short reversal is a 1-reversal or a 2-reversal, i.e., a reversal that affects only one
or two elements of π.
Figure 1 shows a sequence of three super short reversals that transforms the
permutation π = (1 3 4 2 5) with rπ = (3, 5, 2, 1, 2, 8) into ι = (1 2 3 4 5)
with rι = (3, 2, 6, 4, 5, 1).
A pair of elements (πi , πj ) from π is called an inversion if πi > πj and i < j,
with {i, j} ∈ [1..n]. We denote the number of inversions in a permutation π by
inv(π). For the example above, inv(π) = 2.
Given two permutations π and α of same size, representing genomes G1 and G2
respectively, we denote by Wi (π, α) = riπ − riα the imbalance between intergenic
regions riπ and riα , with 1 ≤ i ≤ m.
Super Short Reversals on Both Gene Order and Intergenic Sizes 17
0 3 1 5 3 2 4 1 2 2 5 7 1 6
(a) ρ(5, 5, 2, 7)
0 3 1 5 3 1 1 4 1 2 5 4 5 1 6
(b) ρ(3, 4, 1, 5)
0 3 1 1 4 3 6 2 1 4 5 5 1 6
(c) ρ(2, 3, 1, 1)
0 3 1 2 2 6 3 4 4 5 5 1 6
(d)
Fig. 1. A sequence of super short reversals that transforms π = (1 3 4 2 5), with

rπ = (3, 5, 2, 1, 2, 8) into ι = (1 2 3 4 5), with rι = (3, 2, 6, 4, 5, 1). Intergenic regions
are represented by rectangles, whose dimensions vary according to their sizes. The 1-
reversal ρ(5, 5, 2, 7) applied in (a) transforms π into π = π, and it cuts π after position

2 at r5π and after position 7 at r6π , resulting in r5π = 9, r6π = 1, and rπ = (3, 5, 2, 1, 9, 1).
The 2-reversal ρ(3, 4, 1, 5) applied in (b) transforms π into π = (1 3 2 4 5), and it

cuts π after position 1 at r3π and after position 5 at r5π , resulting in r3π = 6, r5π = 5,

and rπ = (3, 5, 6, 1, 5, 1). Finally, the 2-reversal ρ(2, 3, 1, 1) applied in (c) transforms
π into ι, as shown in (d).
Given two permutations π and α of same size and same total sum of the

j
intergenic region lengths, let Sj (π, α) = Wi (π, α) be the cumulative sum of
i=1
imbalances between intergenic regions of π and α from position 1 to j, with
1 ≤ j ≤ m. Since π and α have same total sum of the intergenic region lengths,
Sm (π, α) = 0.
From now on, we will consider that (i) the target permutation α is such that
α = ι; (ii) π and ι have the same number of elements; and (iii) the number of
nucleotides inside intergenic regions of rπ equals the number of nucleotides inside
intergenic regions of rι . By doing this, we can compute the sorting distance of
π, denoted by d(π), that consists in finding the minimum number of super short
reversals that sorts π and transforms rπ into rι .
The intergenic graph of π with respect to the target permutation ι, denoted
by I(π, ι) = (V, E), is such that V is composed by the set of intergenic regions
rπ and the set of elements from the extended permutation π. Besides, the edge
e = (riπ , ri+2
π
) ∈ E if there is a j = i such that (πi , πj ) or (πj , πi+1 ) is an
inversion, with 1 ≤ i ≤ n−1 and 1 ≤ j ≤ n.
A component c is a minimal set of consecutive elements from V in which: (i)
the sum of imbalances of its intergenic regions with respect to rι is equal to zero;
and (ii) any two intergenic regions that are connected to each other by an edge
must belong to the same component.
18 A. R. Oliveira et al.
c1 e1 e2 c2 e3
0 15 3 6 1 4 2 12 4 8 5 13 7 9 6 2 8
Wi (π, ι) : +5 -9 -4 +5 +3 +4 -4 +0
Si (π, ι) : +5 -4 -8 -3 +0 +4 +0 +0
(a)
c1 c2 e2 c3 e3
0 10 1 6 3 9 2 12 4 8 5 13 7 9 6 2 8
(b)
c1 c2 c3 c4 c5 c6 c7 c8
0 10 1 15 2 8 3 7 4 5 5 9 6 13 7 2 8
(c)
Fig. 2. Intergenic graphs I(π, ι) in (a), I(π , ι) in (b), and I(ι, ι) in (c), with

π = (3 1 2 4 5 7 6), rπ = (15, 6, 4, 12, 8, 13, 9, 2), π = (1 3 2 4 5 7 6), rπ =
ι
(10, 6, 9, 12, 8, 13, 9, 2), ι = (1 2 3 4 5 6 7), and r = (10, 15, 8, 7, 5, 9, 13, 2). Black
squares represent intergenic regions, and the number inside it indicate their sizes.
Rounded rectangles in blue represent components. Note that in (a) there are three
edges in I(π, ι), and C(I(π, ι)) = 2. We also have in (a) all values for Si (π, ι) and
Wi (π, ι), with 1 ≤ i ≤ 8. The permutation π is the result of applying ρ(1, 2, 8, 2) to π.
In (b) we can see that I(π , ι) has one more component than I(π, ι), and the edge e1 was
removed. In (c) we can see that when we reach the target permutation the number of
components is equal to the number of intergenic regions in ι (i.e., C(I(ι, ι)) = m = 8).
A component always starts and finishes with elements from π. Besides, the
first component starts with the element π0 , and the last component ends with
the element πn+1 . Consecutive components share exactly one element from π,
i.e., the last element πi of a component is the first element of its adjacent compo-
nent to the right. A component with one intergenic region is called trivial. The
number of intergenic regions in a component c is denoted by r(c). The number
of components in a permutation π is denoted by C(I(π, ι)). Figure 2 shows three
examples of intergenic graphs.
3 Sorting Permutations by Super Short Reversals

In this section we analyze the version of the problem when only super short
reversals (i.e., 1-reversals and 2-reversals) are allowed to sort a permutation on
both order and intergenic regions. First, we show that any 1-reversal can increase
the number of components by no more than one unit. After that, we state that
if a component c of an intergenic graph I(π, ι) with r(c) > 1 has no edges (i.e.,
there is no inversions inside c), then it is always possible to split c into two
components with a 1-reversal.
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“Yes, sir.” He went back to his hut, delighted.
Escape. Escape. Even the illusion of escape for a few hours, it must
be at least that, for if the 469 Trench Mortar Battery were in the same
Division, the same Corps even, he would have heard of them. They
must be at least a day’s journey away, and he would be able to get
away from the blasting and withering boredom for at least that.
Colonel Birchin, a regular, who had been on various Staff
appointments since the very early days, had no conception how
personnel changed and units shifted, and unless he (Dormer) were
very much mistaken, it would be a jolly old hunt. So much the better.
He would have his mind off the War for a bit.
The reply came from Corps that, according to the order of battle, 469
Trench Mortar Battery was not in existence, but try Trench Mortar
School at Bertezeele. It was all one to Dormer. He might simply be
exchanging one cold hut for another, he might travel by rail and lorry
instead of on horse or foot. But at any rate it would be a different hut
that he was cold in and a different mode of conveyance that jolted
him, and that was something, one must not be too particular in war-
time. So he jumped on a lorry that took him into Doullens and at
Doullens he took train and went through Abbeville and the endless
dumps and camps by the sea, up to Étaples, where the dumps and
camps, the enormous reinforcement depôts and mile-long hospitals
stretched beside the line almost into Boulogne, where was a little
pocket, as it were, of French civilian life, going on undisturbed amid
the general swamping of French by English, on that coast, and of
civilian life by military. Here he got a meal and changed and went off
again up the hill, past Marquise, and down a long hill to Calais, in the
dark, and then on, in the flat, where the country smelled different
from the Somme, and where the people spoke differently and the
names of the stations sounded English, and where there were
French and Belgian police on the platforms.
He slept and woke at St. Omer, and slept again and woke to find all
the lights out and a general scurry and scatteration, with the drone of
aeroplanes and the continual pop-popping of anti-aircraft fire. Then
came the shrieking whirr and sharp crash of the first bomb, with its
echo of tinkling glass, barking of dogs, and rumour of frightened
humanity.
Like most people accustomed to the line, Dormer regarded the
bombing of back billets as a spectacle rather than as one of the
serious parts of warfare, and got out to stroll about the platform with
officers going up as reinforcements. They exchanged cigarettes and
news and hardly stopped to laugh at the horrified whisper of the
R.T.O., “Don’t light matches here!” It was soon over, like all bombing.
If you were hit you were hit, but if you weren’t hit in the first minute or
two, you wouldn’t be, because no plane could stay circling up there
for very long, and the bomber was always more frightened than you
were. Then the train moved on, and Dormer could feel on each side
of him again the real camp life of units just behind the line, mule
standings, gun parks, and tents and huts of infantry, and services. It
was midnight before he got out at Bailleul. He had left the camp on
the Arras road in the morning, had made a great loop on the map
and reached a railhead as near the line as he had been twenty-four
hours before. He stumbled up the stony street to the Officers’ Rest
House, drank some cocoa out of a mug and fell asleep, his head on
his valise.
In the morning he got a lift out to Bertezeele, and found the Trench
Mortar School. He reflected that it would really be more correct to
say that he took a lift to the Trench Mortar School, and incidentally
touched the village of Bertezeele. For the fact was that the English
population of the parish exceeded the French native one. Men of all
sorts and conditions from every unit known to the Army List (and a
good many that had never graced the pages of that swollen
periodical) were drawn into this new device for improved killing.
Dormer himself, one of those who, since the elementary home camp
training of 1915, had been in or just behind the trenches, wondered
at the complicated ramifications with which the War was running.
Apparently those curious little brass instruments, the bane of his life
as an infantry platoon commander, which used to come up behind
his line and there, while totally ineffective in the vital matter of
beating the Germans, were just sufficiently annoying to make those
methodical enemies take great pains to rob him of his food and sleep
for many ensuing days, were all done away with.
Stokes, whoever he was, but he was certainly a genius, had effected
a revolution. Owing to him, neat tubes, like enlarged pencil-guards,
with a nail inside the blind end, upon which the cap-end of the
cartridge automatically fell, were being used, as a hosier might say,
in all sizes from youths’ to large men’s. Stokes was branded with
genius, because his invention combined the two essentials—
simplicity with certainty. He had brought the blunderbuss up to date.
What else were these short-range, muzzle-loading, old-iron
scattering devices? Just blunderbusses. History was not merely
repeating itself. As the War went on it was moving backwards. Tin
helmets of the days of Cromwell, bludgeons such as Cœur de Lion
used upon Saladin, and for mere modernity, grenades like the
original British Grenadiers of the song. He had never had any head
for poetry, but he could remember some of the stuff Kavanagh had
sung in the dug-out. Not tow-row-row. That was the chorus. Ah! he
remembered.
“Our leaders march with fusees,
And we with hand-grenades,
We throw them from the glacis
About the enemy’s ears.
With a tow-row-row,” etc.
Well, now we didn’t. If we had grenades we carried them in aprons,
like a market woman, with a skirt full of apples. And if we had a
blunderbuss, like the guard of the coach in the “Pickwick Papers,” we
kept it, and all the ironmongery that belonged to it, on a hand-barrow,
and pushed it in front of us like fish-hawkers on a Saturday night.
What a War! Kavanagh was quite right of course. There was neither
decency nor dignity left in it. Wouldn’t do to admit that though! And
putting on his very best “Good-mornin’-Sah-I-have-been-sent-by-
Divisional-Head-quarters” expression, he asked his way to the
“office” as they were beginning to call the orderly room in most
detachments, and inquired for 469 Battery. Yes. They were to be
seen. Orderly room, as a Corps formation, was distant and slightly
patronizing, but the information was correct. He could see the Officer
commanding the battery. Certainly he could, as soon as morning
practice was over. That would do. He made himself as
inconspicuous as possible until he saw the various parties being
“fallen in” on the range, and heard the uncanny ear-tickling silence
that succeeded the ceaseless pop-pop of practice and then drifted
casually into the wooden-chair-and-table furnished ante-room, where
the month-old English magazines gave one a tremulous home-
sickness, and men who had been mildly occupied all the morning
were drinking all the vermouth or whisky they could, in the fear of
being bored to the point of mutiny in the afternoon.
There was, of course, the usual springtime curiosity as to what the
year might bring forth, for every one always hoped against hope that
the next offensive would really be the last. An orderly wandering
among the tables appeared to be looking for him, and he found
himself summoned before the Officer commanding the School.
Although his appointment was new, Colonel Burgess was of the
oldest type of soldier, the sort who tell the other fellows how to do it.
The particular sort of war in which he found himself suited him
exactly. He had the true Indian view of life, drill, breakfast, less drill,
lunch, siesta, sport, dinner, cards. So he ruled the mess cook with a
rod of iron, took disciplinary action if the stones that lined the path
leading to the door of the ante-room and office were not properly
white, and left the technical side of the business to Sergeant-
instructors who, having recently escaped from the trenches, were
really keen on it.
He received Dormer with that mixture of flattery due to anyone from
Divisional Head-quarters and suspicion naturally aroused as to what
he (Dormer) might be after. He was annoyed that he had not heard
of Dormer’s arrival, and hastened to add:
“Not a very full parade this morning, units come and go, y’know. We
can never be quite sure what we are going to get! What did you think
of our show?”
Dormer realized that the old gentleman was under the impression he
was being spied on:
“I really didn’t notice, sir. I have been sent to see the Officer
commanding 469 Trench Mortar Battery. Matter of discipline arising
out of a claim for compensation.”
“Oh, ah! Yes indeed. Certainly. See him now. Sergeant Innes!”
The efficient Scotch Sergeant to be found in all such places
appeared from the outer office.
“Have we anyone here from 469 T.M.B.?”
The officer required was duly produced, and the Colonel retired to
the Mess, leaving them together. Dormer sized up this fellow with
whom he was thus brought into momentary contact. This became by
necessity almost a fine art, during years of war. Dormer was fairly
proficient. The fellow opposite to him was of the same sort as
himself. Probably in insurance or stockbroking, not quite the
examination look of the Civil Service, not the dead certainty of
banking. He had obviously enlisted, been gradually squeezed up to
the point of a Commission, had had his months in the line and had
taken to Trench Mortars because they offered the feeling of really
doing something, together with slightly improved conditions (hand-
carts could be made to hold more food, drink and blankets than mere
packs) and was getting along as well as he could. He heard what
Dormer wanted and his face cleared.
“Why, that’s last April. I couldn’t tell you anything about that. I was in
Egypt!”
“You don’t know of any officer in your unit who could give some
information about the occurrence?”
“No. There’s only young Sands, beside myself. He couldn’t have
been there.”
“Some N.C.O. then?”
“Heavens, man, where d’you think we’ve been? All the N.C.O.’s are
new since I was with the crowd!”
“But surely there must be some record of men who were with your
unit?”
“Well, of course, the pay rolls go back to Base somewhere. But I
suppose you can pick the name and number up from the conduct
sheet.”
“You see, I don’t know the man’s name. His number was given as
6494.”
“That’s a joke, of course. It’s the number that the cooks sing out,
when we hold the last Sick Parade, before going up the line.”
“Of course it is. You’re right. I ought to have remembered that, but
I’ve been away from my regiment for some time.” Dormer pondered
a moment, relieved. Then the thought of going back to the Q. office
with nothing settled, and the queries of the French Mission and the
whole beastly affair hanging over his head, drove him on again. He
made his air a little heavier, more Divisional, less friendly.
“Well, I’m afraid this won’t do, you know. This matter has got to be
cleared up. It will be very awkward if I have to go back and inform
Head-quarters that you can’t furnish any information. In fact, they will
probably think it’s a case of not wanting to know, and make a regular
Court of Inquiry of it.”
He watched the face of the other, and saw in a moment how well he
had calculated. The fellow was frightened. A mere unit commander,
and a small unit at that! To such a one, of course, Divisional Head-
quarters were something pretty near omniscient, certainly
omnipotent. Dormer watched the fellow shift in the chair without a
qualm. Let some one else be worried too. He himself had had worry
enough. The face before him darkened, smirked deferentially, and
then brightened.
“Oh, there was old Chirnside. He might know.”
“Who was he?”
“Chirnside? He was a sort of a quarter bloke. It was before we were
properly formed, and he used to look after all our stores and orderly
room business. He had been with the battery since its formation. We
were just anybody, got together anyhow, chiefly from the infantry, you
remember?”
Dormer saw the other glance at his shoulder straps and just refrain
from calling him sir, poor wretch. He took down the information and
thanked his friend. Chirnside had apparently gone to some stunt
Corps, to do something about equipment. That was all right. He
wouldn’t be killed.
Having got thus far, Dormer felt that he had done a good deal, and
went to take his leave of Colonel Burgess. But he soon found that he
was not to be allowed to get away like that. He was bidden to stay to
lunch. There was no train from Bailleul until the evening and he was
willing enough. The lunch was good. Food remained one of the
things in which one could take an interest. He did so. After lunch the
Colonel took him for a walk over the golf course. This was the
margin of land around the range, on which no cultivation was
allowed, and from which civilians were rigidly excluded, for safety’s
sake. At least during range practice, which took place every day
more or less, in the morning. After that, of course, they could be
without difficulty excluded for the remainder of the day for a different,
if not for so laudable a purpose.
The Colonel was a fine example of those qualities which have made
an island Empire what it is. Having spent most of his life from sixteen
years old at Sandhurst, then in India or Egypt, and finally at
Eastbourne, he knew better than most men how to impose those
institutions which he and his sort considered the only ones that made
civilization possible, in the most unlikely places and upon the most
disinclined of people. Dormer had seen it being done before, but
marvelled more and more. Just as the Colonel, backed of course by
a sufficient number of his like, and the right sort of faithful underling,
had introduced tennis into India, duck-shooting into Egypt, and
exclusiveness into Eastbourne, against every condition of climate or
geographical position, native religion or custom, so now he had
introduced golf into Flanders, and that in the height of a European
War.
At the topmost point of the golf course, the Colonel stopped, and
began to point out the beauties of the spot to Dormer. They were
standing on one of those low gravelly hills that separate the valley of
the Yser from that of the Lys. Northward, beyond Poperinghe, was a
yet lower and greener ridge that shelved away out of sight toward
Dunkirk. East lay Ypres, in an endless rumour of war. Southward, the
Spanish towers of Bailleul showed where the road wound towards
Lille, by Armentières. Westward, Cassel rose above those hillocks
and plains, among the most fertile in the world. But the Colonel was
most concerned with a big square old farmhouse, that lay amid its
barns and meadows, at a crook in the Bailleul road.
The Colonel’s eyes took on a brighter blue and his moustache puffed
out like fine white smoke.
“I had a lot of trouble with that fellow.” He pointed to the farm.
“Wanted to come and cultivate the range. I had to get an interpreter
to see him. Said he could grow—er—vegetables in between the
shell-holes. At last we had to order afternoon practice to keep him
off. Then he wanted this part of the land. Had to move the guns up
and make some new bunkers. Four rounds makes a bunker, y’know.
Come and have tea?”
It was very nice weather for walking, dry and clear. The Mess had
seemed tolerable at lunch, but Dormer had not been long at tea
before he recollected what he seldom forgot for more than an hour or
so, that it was not tea, one of the fixed occasions of his safe and
comfortable life. It was a meal taken under all the exigencies of a
campaign—chlorinated water, condensed milk, army chair, boots and
puttees on one, and on this particular afternoon a temperature below
zero, in an army hut.
The Colonel, of course, occupied the place of warmth next the stove.
The remainder of the Mess got as near to it as they could. The result
was, that when the Colonel began to question him as to the object of
his visit, and how he had progressed towards attaining it, everybody
necessarily heard the whole of the conversation. He now realized
that he was telling the tale for the fourth time. He had told it to
Kavanagh, then to Colonel Birchin. Now he had told it to the Officer
commanding 469 T.M.B. and finally here he was going over it again.
He resented it as a mere nuisance, but was far from seeing at that
moment the true implication of what he was doing. The matter was
not a State secret. It was an ordinary piece of routine discipline,
slightly swollen by its reactions in the French Mission, and by the
enormous size and length of the War.
If he had refused to say why he was there the Colonel would
certainly have put him down as having been sent by the Division, or
some one even higher, to spy on the activities of the School. He
didn’t want to be labelled as that, so told what he knew glibly
enough. The Colonel waxed very voluble over it, gave good advice
that was no earthly use, and dwelt at length on various aspects of
the case. The French were grasping and difficult and superstitious,
but on the other hand, drivers were a rough lot and must be kept in
check. They were always doing damage. The fellow was quite right
of course to look after his mules. The animals were in a shocking
state, etc., etc., but quite wrong, of course, to damage civilian
property, tradition of the British Army, since Wellington all the other
way, the French naturally expected proper treatment, etc., etc.
Dormer had heard it all before, from Colonel Birchin, Major
Stevenage and others, with exactly the same well-meant
condescension, and the same grotesque ineffectiveness. This old
Colonel, like all his sort, couldn’t solve the difficulty nor shut the
French up, nor appease G.H.Q.
Presently, the old man went off to the orderly room to sign the day’s
correspondence, the Mess thinned and Dormer dozed discreetly, he
had had a poor night and was desperately sleepy. Some one came
to wake him up and offered him a wash, and he was glad to move,
stiff with cold, and only anxious to pass the time until he could get
the midnight train from Bailleul. They were very hospitable, made
much of him at dinner, and he ate and drank all he could get, being
ravenous and hoping to sleep through the discomforts of the long
train journey in the dark. He was getting fairly cheerful by the time
the Colonel left the hut, and only became conscious, in the intervals
of a learned and interesting discussion of the relative theories of
wire-cutting, that a “rag” was in progress at the other end of the
room.
A gunner officer, a young and happy boy who was still in the stage of
thinking the War the greatest fun out, was holding a mock Court of
Inquiry. Gradually, the “rag” got the better of the argument and
Dormer found himself being addressed as “Gentlemen of the jury.” A
target frame was brought in by some one to act as a witness-box,
but the gunner genius who presided, soon had it erected into a sort
of Punch and Judy Proscenium. Then only did it dawn on Dormer
that the play was not Punch and Judy. It was the Mayor of
Hondebecq being derided by the troops, with a Scotch officer in a kilt
impersonating Madeleine Vanderlynden, and receiving with the
greatest equanimity, various suggestions that ranged from the feebly
funny to the strongly obscene. O.C. 469 T.M.B. found a willing
column formed behind him which he had to lead round the table, an
infantryman brought a wastepaper basket to make the Mayor’s top
hat, and in the midst of other improvisations, Dormer discovered the
gunner standing in front of him with a mock salute.
“Do you mind coming out of the Jury and taking your proper part?”
It was cheek, of course, but Dormer was not wearing red tabs, and
beside, what was the use of standing on one’s dignity. He asked:
“What part do I play?”
“You’re Jack Ketch. You come on in the fourth Act, and land Nobby
one on the nob!”
“I see. What are you?”
“Me? I’m the Devil. Watch me devilling,” and with a long map-roller
he caught the players in turn resounding cracks upon their several
heads.
They turned on him with common consent, and in the resulting
struggle, the table broke and subsided with the whole company in an
ignominious mass. The dust rose between the grey canvas-covered
walls and the tin suspension lamp rocked like that of a ship at sea.
Everybody picked themselves up, slightly sobered, and began to
discuss how to get the damage repaired before the Colonel saw it in
the morning.
O.C. 469 T.M.B. stood at Dormer’s elbow:
“We’ve just got time to catch your train.”
“Come on.” Dormer had no intention of being marooned in this place
another day. Outside a cycle and side-car stood panting. Dormer did
wonder as they whizzed down the rutted road how long such a
vehicle had been upon the strength of a Trench Mortar School, but
after all, could you blame fellows? They were existing under War
conditions, what more could one ask?
He woke to the slow jolting of the train as it slowed up in smoky

twilight at Boulogne. He bought some food, and sitting with it in his
hands and his thermos between his knees, he watched the grey
Picard day strengthen over those endless camps and hospitals,
dumps and training grounds.
He was retracing his steps of the day before, but he was a step
farther on. As he looked at the hundreds of thousands of khaki-clad
figures, he realized something of what he had to do. With no name
or number he had to find one of them, who could be proved to have
been at a certain place a year ago. He didn’t want to, but if he didn’t,
would he ever get rid of the business?
The “rag” of the previous evening stuck in his head. How true it was.
The man who did the thing was “Nobby” with the number 6494 that
was beginning to be folk-lore. Of course he was. He was any or
every soldier. Madeleine Vanderlynden was the heroine. O.C. 469
T.M.B. was the hero. The Mayor of Hondebecq was the comic relief,
and he, Dormer, was the villain. He was indeed Jack Ketch, the
spoiler of the fun, the impotent figure-head of detested “Justice,” or
“Law and Order.” And finally, as in all properly conducted Punch and
Judy shows, the Devil came and took the lot. What had Dendrecourt
said: “The Devil had taken the whole generation.” Well, it was all in
the play. And when he realized this, as he slid on from Étaples down
to Abbeville, he began to feel it was not he who was pursuing some
unknown soldier in all that nation-in-arms that had grown from the
British Expeditionary Force, but the Army—no, the War—that was
pursuing him.
When he got out at Doullens, and scrounged a lift from a passing
car, he found himself looking at the driver, at the endless transport
on either side of the road, at the sentry on guard over the parked
heavies in the yard of the jam factory, at the military policeman at the
cross-roads. One or other of all these hundreds of thousands knew
all about the beastly business that was engaging more and more of
his mind. One or other of them could point to the man who was
wanted.
He found himself furtively examining their faces, prepared for covert
ridicule and suspicion, open ignorance or stupidity. He had, by now,
travelled a long way from the first feelings he had about the affair,
when he had thought of the perpetrator of the damage at
Vanderlynden’s as a poor devil to be screened if possible. He
wouldn’t screen him now. This was the effect of the new possibility
that had arisen. He, Dormer, did not intend to be ridiculous.
On reaching the Head-quarters of the Division, he found the War in
full progress. That is to say, every one was standing about, waiting to
do something. Dormer had long discovered that this was war.
Enlisting as he had done at the outbreak of hostilities, with no actual
experience of what such a set of conditions could possibly be like, he
had then assumed that he was in for a brief and bitter period of
physical discomfort and danger, culminating quite possibly in death,
but quite certainly in a decisive victory for the Allies within a few
months. He had graduated in long pedestrian progress of Home
Training, always expecting it to cease one fine morning. It did. He
and others were ordered to France. With incredible slowness and
difficulty they found the battalion to which they were posted. Now for
it, he had thought, and soon found himself involved in a routine,
dirtier and more dangerous, but as unmistakably a routine as that in
which he had been involved at home.
He actually distinguished himself at it, by his thoroughness and care,
and came to be the person to whom jobs were given! Thus had he
eventually, after a twelvemonth, found another false end to the
endless waiting. He was sent to help the Q. office of Divisional Staff.
He had felt himself to be of considerable importance, a person who
really was winning the War. But in a few weeks he was as disabused
as ever. It was only the same thing. Clerking in uniform, with no
definite hours, a few privileges of food and housing, but no nearer
sight of the end of it. The Somme had found him bitterly
disillusioned. And yet even now, after being two days away from the
Head-quarters where his lot was cast, he was dumbfounded afresh
to find everything going on just as he had left it.
They were all waiting now for orders to go into a back area and be
trained. For, as sure as the snowdrop appeared, there sprang up in
the hearts of men a pathetic eternal hopefulness. Perhaps nothing
more than a vernal effusion, yet there it was, and as Dormer
reported to Colonel Birchin, in came the messenger they had all
been expecting, ordering them, not forward into the line, but
backward to Authun, for training. It was some time before he could
get attention, and when he did, it seemed both to him and to the
Colonel that the affair had lessened in importance.
“You’ve asked 3rd Eccleton to give you the posting of this
Chirnside?”
“Yessir!”
“Very well. That’s all you can do for the moment. Now I want you to
see that everything is cleared up in the three Infantry Brigade camps,
and don’t let us have the sort of chits afterwards that we got at
Lumbres, etc.”
So the Vanderlynden affair receded into the background, and
Dormer found before his eyes once more that everlasting mud-
coloured procession, men, men, limbers, cookers, men, lorries,
guns, limbers, men.
He looked at it this time with different eyes. His Division was one-
fiftieth part of the British Army in France. It took over a day to get on
the move, it occupied miles of road, absorbed train-loads of supplies,
and would take two days to go thirty miles. The whole affair was so
huge, that the individual man was reduced and reduced in
importance until he went clean out of sight. This fellow he was
pursuing, or Chirnside, or anyone who could have given any useful
information about the Vanderlynden claim, might be in any one of
those cigarette-smoking, slow-moving columns, on any of those
springless vehicles, or beside any of those mules.
He gazed at the faces of the men as they streamed past him, every
county badge on their caps, every dialect known to England on their
lips, probably the best natured and easiest to manage of any of the
dozen or so national armies engaged in the War. He was realizing
deeply the difficulty of discovering that particular “Nobby” who had
broken the front of the shrine at Vanderlynden’s. It was just the thing
any of them would do. How many times had he noticed their curious
tenderness for uncouth animals, stray dogs or cats, even moles or
hedgehogs, and above all the brazen, malevolent army mule. He
was no fancier of any sort of beast, and the mule as used in France
he had long realized to have two virtues and two only—cheapness
and durability. You couldn’t kill them, but if you did, it was easy to get
more. He had been, for a long while now, a harassed officer, busy
shifting quantities of war material, human, animal, or inanimate, from
one place to another, and had come to regard mules as so much
movable war stores. Added to the fact that he was no fancier, this
had prevented him from feeling any affection for the motive power of
first-line transport. But he was conscious enough that it was not so
with the men—the “other ranks” as they were denominated in all
those innumerable parade states and nominal rolls with which he
spent his days in dealing.
No, what the fellow had done was what most drivers would do. That
queer feeling about animals was the primary cause of the whole
affair. Then, balancing it, was the natural carelessness about such
an object as a shrine—this same brown-clothed nation that defiled
before him, he knew them well. As a churchwarden, he knew that not
ten per cent of them went inside a place of worship more than three
or four times in the whole of their lives. Baptism for some, marriage
for a good proportion, an occasional assistance at the first or last rite
of some relative, finally, the cemetery chapel, that was the extent of
their church-going.
A small number, chiefly from the North or from Ireland, might be
Catholics, but also from the north of Ireland was an equal number of
violent anti-Catholics, and it was to this latter section that he judged
the perpetrator of the outrage to belong. No, they would see nothing,
or at best something to despise, in that little memorial altar, hardly
more than an enlarged tombstone, in the corner of a Flemish
pasture. It was strange if not detestable, it was foreign; they never
saw their own gravestones, seldom those of any relative. He
sympathized with them in that ultra-English sentimentality, that
cannot bear to admit frankly the frail briefness of human life. And so
the thing had happened, any of them might have done it, most of
them would do it, under similar circumstances.
The tail of the last column wound out of B camp, the N.C.O. he took
with him on these occasions was reporting all clear, and might he
hand over to the advance party of the incoming Division. Dormer
gave him exact orders as to what to hand over and obtain a
signature for, and where to find him next, for he did not believe in
allowing an N.C.O. any scope for imagination, if by any possibility
such a faculty might have survived in him.
The weather had broken, and he jogged along in the mud to C camp
and found it already vacated, but no advance party ready to take
over, and resigned himself to the usual wait. He waited and he
waited. Of course, he wasn’t absolutely forced to do so. He might
have left his N.C.O. and party to hand over. He might have cleared
them off and left the incoming Division to shift for itself. That had
been done many a time in his experience. How often, as a platoon
commander, had he marched and marched, glancing over his
shoulder at tired men only too ready to drop out, marched and
marched until at length by map square and horse sense, and general
oh-let’s-get-in-here-and-keep-any-one-else-out, he had found such a
camp, a few tents subsiding in the mud, a desolate hut or two,
abandoned and unswept, places which disgusted him more than any
mere trench or dug-out, because they were places that people had
lived in and left unclean.
He had never experienced such a thing before he came into the
army. His nice middle-class upbringing had never allowed him to
suspect that such places existed. And now that he was Captain
Dormer, attached H.Q. Nth Division, he endeavoured to see that they
did not. So he hung about intending to see the thing done properly.
He got no encouragement. He knew that when he got back to the
Division Colonel Birchin would simply find him something else to do,
and the fact that no complaints followed them, and that the incoming
Division had a better time than they would otherwise have had,
would be swallowed up in the hasty expedience of the War. Still, he
did it, because he liked to feel that the job was being properly done.
To this he had been brought up, and he was not going to change in
war-time.
As he hung about the empty hut, he had plenty of time for reflection.
His feet were cold. When would he get leave? What a nuisance if
these d——d people who were relieving him didn’t turn up until it
was dark. The February day was waning. Ah, here they were. He
roused himself from the despondent quiescence of a moment ago,
into a crisp authoritative person from Divisional Head-quarters.
Never was a camp handed over more promptly. He let his N.C.O.
and men rattle off in the limber they had provided themselves with.
He waited for a car. There was bound to be no difficulty in getting a
lift into Doullens, and if he did not find one immediately there, he
would soon get a railway voucher. As he stood in the gathering dusk
his ruminations went on. If it were not for the War, he would be going
home to tea, real proper tea, no chlorine in the water, milk out of a
cow, not out of a tin, tea-cakes, some small savoury if he fancied it,
his sister with whom he lived believing in the doctrine. “Feed the
beast!” After that, he would have the choice of the Choral Society or
generally some lecture or other. At times there was something on at
the local theatre, at others he had Vestry or Trust meetings to attend.
Such employments made a fitting termination to a day which he had
always felt to be well filled at a good, safe, and continuous job, that
would go on until he reached a certain age, when it culminated in a
pension, a job that was worth doing, that he could do, and that the
public appreciated.
Instead of all this, here he was, standing beside a desolate Picard
highway, hoping that he might find his allotted hut in time to wash in
a canvas bucket, eat at a trestle table and finally, having taken as
much whisky as would wash down the food, and help him to become
superior to his immediate circumstances, to play bridge with those
other people whom he was polite to, because he had to be, but
towards whom he felt no great inclination, and whom he would drop
without a sigh the moment he was demobbed.
Ah! Here was the sort of car. He stepped into the road and held up
his hand. The car stopped with a crunch and a splutter. They were
going as far as Bernaville. That would suit him well. He jammed into
the back seat between two other people, mackintoshed and goggled,
and the car got under way again. Then he made the usual remarks
and answered the usual inquiries, taking care to admit nothing, and
to let his Divisional weight be felt. Finally he got down at a place
where he could get a lorry lift to H.Q.
His servant had laid out some clean clothes in the Armstrong hut.
For that he was thankful.
The Division now proceeded to train for the coming offensive.

“Cultivators” had been warned off a large tract of land, which was
partly devoted to “Schools,” at which were taught various superlative
methods of slaughter, partly to full-dress manœuvres over country
which resembled in physical features the portion of the German line
to be attacked. The natural result was that if any area larger than a
tennis court was left vacant, the “cultivators” rushed back and began
to cultivate it. Hence arose disputes between the peasants and the
troops, and the General commanding the 556 Brigade had his bridle
seized by an infuriated female who wanted to know, in English, why
he couldn’t keep off her beans.
The matter was reported to G. office of Divisional Head-quarters,
who told the A.P.M., who told the French Liaison Officer, who told an
Interpreter, who told the “cultivators” to keep off the ground
altogether, whether it were in use or not. In revenge for which
conduct the “cultivators” fetched the nearest gendarme, and had the
Interpreter arrested as a spy, and tilled the land so that the C.R.A.
Corps couldn’t find the dummy trenches he was supposed to have
been bombarding, because they had all been filled up and planted.
So that he reported the matter to Corps, who sat heavily on
Divisional Head-quarters, G. office, for not keeping the ground clear.
The A.P.M. and French Mission having been tried and failed, Q.
office had the brilliant idea of “lending” Dormer to G., upon the well-
tried army principle that a man does a job, not because he is fit, but
because he is not required elsewhere.
So Dormer patrolled the manœuvre area, mounted on the horses of
senior officers, who were too busy to ride them. He did not object. It
kept him from thinking. He was, by now, well acquainted with
manœuvre areas, from near Dunkirk to below Amiens. It was the
same old tale. First the various schools. The Bombing Instructor
began with a short speech:
“It is now generally admitted that the hand-grenade is the weapon
with which you are going to win this War!”
The following day in the bayonet-fighting pitch, the instructor in that
arm began:
“This is the most historic weapon in the hands of the British Army. It
still remains the decisive factor on the field!”
And the day following, on the range, the Musketry expert informed
the squad:
“Statistics show that the largest proportion of the casualties inflicted
on the enemy are bullet wounds.”
Dormer was not unkind enough to interrupt. He did not blame those
instructors. Having, by desperately hard work, obtained their
positions, they were naturally anxious to keep them. But his new
insight and preoccupation, born of the Vanderlynden affair, made him
study the faces of the listening squads intently. No psychologist, he
could make nothing of them. Blank, utterly bored in the main, here
and there he caught sight of one horrified, or one peculiarly
vindictive. The main impression he received was of the sheer
number of those passive listening faces, compared with the fewness
of the N.C.O.’s and instructors. So long as they were quiescent, all
very well. But if that dormant mass came to life, some day, if that
immense immobility once moved, got under way, where would it
stop?
It was the same with the full-dress manœuvres. Dormer had never
been taken up with the honour and glory of war. He was going
through with this soldiering, which had been rather thrust upon him,
for the plain reason that he wanted to get to the end of it. He
considered that he had contracted to defeat the Germans just as, if
he had been an iron firm, he might have contracted to make girders,
or if he had been the Post Office, he would have contracted to
deliver letters. And now that he watched the final processes of the
job, he became more than ever aware that the goods would not be
up to sample. How could they be? Here were men being taught to
attack, with the principal condition of attack wanting. The principal
condition of an attack was that the other fellow hit you back as hard
as he could. Here there was no one hitting you back. He wondered if
all these silent and extraordinarily docile human beings in the ranks
would see that some day. He looked keenly at their faces. Mask,
mask; mule-like stupidity, too simple to need a mask; mask and
mask again; one with blank horror written on it, one with a devilish
lurking cunning, as if there might be something to be made out of all
this some day; then more masks.
He wondered, but he did not wonder too unhappily. He was
beginning to feel very well. Away from the line, the hours were more
regular, the food somewhat better, the horse exercise did him good.
There was another reason which Dormer, no reader of poetry, failed
altogether to appreciate. Spring had come. Furtive and slow, the
Spring of the shores of the grey North Sea came stealing across
those hard-featured downs and rich valleys. Tree and bush,
blackened and wind-bitten, were suddenly visited with a slender
effusion of green, almost transparent, looking stiff and ill-assorted, as
though Nature were experimenting.
Along all those ways where men marched to slaughter, the magic
footsteps preceded them, as though they had been engaged in some
beneficent work, or some joyful festival. To Dormer the moment was
poignant but for other reasons. It was the moment when the
culminating point of the Football Season marked the impending truce
in that game. He did not play cricket. It was too expensive and too
slow. In summer he sailed a small boat on his native waters. Instead,
he was going to be involved in another offensive.
The Division left the manœuvre area and went up through Arras. Of
course, the weather broke on the very eve of the “show.” That had
become almost a matter of routine, like the shelling, the stupendous
activities of railways and aeroplanes, the everlasting telephoning.
Again Dormer saw going past him endlessly, that stream of men and
mules, mules and men, sandwiched in between every conceivable
vehicle, from tanks to stretchers. When, after what communiqués
described as “continued progress” and “considerable artillery
activity,” it had to be admitted that this offensive, like all other
offensives, had come to a dead stop, Dormer was not astonished.
For one thing, he knew, what no communiqué told, what had stopped
it. The Germans? No, capable and determined as they were. The
thing which stopped it was Mud. Nothing else. The shell-fire had
been so perfect, that the equally perfect and necessarily complicated
preparations for going a few hundred yards farther, could not be
made. The first advance was miles. The next hundreds of yards. The
next a hundred yards.
Then the Bosche got some back. Then everything had to be moved
up to make quite certain of advancing miles again. And it couldn’t be
done. There was no longer sufficient firm ground to bear the tons of
iron that alone could help frail humanity to surmount such efforts.
For another thing, he could not be astonished. For weeks he worked
eighteen hours a day, ate what he could, slept when he couldn’t help
it. Astonishment was no longer in him. But one bit of his mind
remained, untrammelled by the great machine of which he formed an
insignificant part. It was a bit of subconsciousness that was always
listening for something, just as, under long-range, heavy-calibre
bombardment, one listened and listened for the next shell. But the
particular detached bit of Dormer was listening and listening for
something else. Watching and watching, too, all those faces under
tin helmets, and just above gas-mask wallets, all so alike under
those conditions that it seemed as difficult to pick out one man from
another as one mule from another. Listening for one man to say “I

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Advances in Bioinformatics and

Computational Biology 11th Brazilian

GeNeDis 2018 Computational Biology and Bioinformatics

11th International Conference on Practical Applications

Advances in Visual Computing 13th International

Advances in Computational Intelligence 17th Mexican

Challenges and Opportunities in the Digital Era: 17th

Advances in Computational Intelligence Proceedings of

Practical Applications of Computational Biology and

Relational and Algebraic Methods in Computer Science

Subseries of Lecture Notes in Computer Science

LNBI Series Editors

LNBI Editorial Board

ISSN 0302-9743 ISSN 1611-3349 (electronic)

Library of Congress Control Number: 2018956561

LNCS Sublibrary: SL8 – Bioinformatics

© Springer Nature Switzerland AG 2018

November 2018 Ronnie Alves

Local Organizing Committee

Fabrício Martins Lopes Universidade Federal Tecnológica do Paraná, Brazil

Sociedade Brasileira de Computação (SBC)

Sorting k-Permutations by k-Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Super Short Reversals on Both Gene Order and Intergenic Sizes. . . . . . . . . . 14

Identifying Maximal Perfect Haplotype Blocks . . . . . . . . . . . . . . . . . . . . . . 26

Sorting by Weighted Reversals and Transpositions . . . . . . . . . . . . . . . . . . . 38

Graph Databases in Molecular Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

ViMT - Development of a Web-Based Vivarium Management Tool . . . . . . . 58

An Argumentation Theory-Based Multiagent Model to Annotate Proteins . . . 66

AutoModel: A Client-Server Tool for Intuitive and Interactive

Detecting Acute Lymphoblastic Leukemia in down Syndrome Patients

S2 FS: Single Score Feature Selection Applied to the Problem of

A Genetic Algorithm for Character State Live Phylogeny. . . . . . . . . . . . . . . 114

A Workflow for Predicting MicroRNAs Targets via Accessibility

Parallel Solution Based on Collective Communication Operations

Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

Guilherme Henrique Santos Miranda1(B) ,

Abstract. The understanding of how diﬀerent two organisms are is one

Keywords: Genome rearrangements · Approximation algorithms

Depending on the genomic information available and the problems consid-

3 Inversions-Based Approximation Algorithms

Lemma 2. Let π be a λ-permutation. It is always possible to obtain a λ-

Proof. Let πj = i be the smallest element out-of-place (πi = i) in π. Initially,

A generic greedy approximation algorithm for the three problems we are

Theorem 3. There exist O(λ2 )-approximation algorithms for the problems of

Proof. Let λ ≥ 2 be an integer and let π = ι be a λ-permutation. Consider an

4 Breakpoints-Based Approximation Algorithms

In this section we present approximation algorithms based on the concept of

A maximal subsequence (πi πi+1 . . . πj ) without any breakpoints (πk , πk+1 ),

Lemma 5. Let π be a λ-permutation and let πj = i be the smallest element

Proof. First, suppose we have S = (πj . . . πk ) as an increasing strip. Then,

In next lemma, we suppose that the smallest element out-of-place is in an

Lemma 6. Let π be a λ-permutation. Let πj = i be the smallest element out-

Lemma 7. Let π be a λ-permutation. Let πj = i be the smallest element out-

Lemma 8. Let π be a λ-permutation. Let πj = i be the smallest element out-of-

Lemma 9. Let πk = i be the smallest element out-of-place in a λ-permutation

Next theorems describe approximation algorithms for the problems we are

Lemma 10. Let π be a λ-permutation. Let S = (j . . . i) be a decreasing strip

Theorem 11. The problem of Sorting λ-Permutations by λ-Reversals has a

Proof. Let λ ≥ 2 be an integer and π = ι be a λ-permutation. Consider an

Theorem 12. The problem of Sorting λ-Permutations by λ-Transpositions has

Proof. Let λ ≥ 2 be an integer and let π = ι be a λ-permutation. The algo-

Theorem 13. The problem of Sorting λ-Permutations by λ-Reversals and λ-

Proof. Let λ ≥ 2 be an integer and let π = ι be a λ-permutation. Let πj = i

We have implemented the inversions-based and the breakpoints-based approxi-