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 Teresa M. Przytycka (Ed.)

Research
LNBI 9029

in Computational
Molecular Biology
19th Annual International Conference, RECOMB 2015
Warsaw, Poland, April 12–15, 2015
Proceedings

123
Lecture Notes in Bioinformatics 9029

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

Alberto Apostolico
Georgia Institute of Technology, Atlanta, GA, USA
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, 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, 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
Teresa M. Przytycka (Ed.)

Research
in Computational
Molecular Biology
19th Annual International Conference, RECOMB 2015
Warsaw, Poland, April 12–15, 2015
Proceedings

ABC
Editor
Teresa M. Przytycka
National Center for Biotechnology Information
Bethesda
Maryland
USA

ISSN 0302-9743 ISSN 1611-3349 (electronic)

Lecture Notes in Bioinformatics
ISBN 978-3-319-16705-3 ISBN 978-3-319-16706-0 (eBook)
DOI 10.1007/978-3-319-16706-0

Library of Congress Control Number: 2015934031

LNCS Sublibrary: SL8 – Bioinformatics

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 Preface

The RECOMB conference series – with the full name of the Annual International Con-
ference on Research in Computational Molecular Biology – was started in 1997 by
Sorin Istrail, Pavel Pevzner, and Michael Waterman. The 19th RECOMB conference,
RECOMB 2015, was held in Warsaw, Poland during April 12–15, 2015 and was hosted
by the University of Warsaw.
This volume contains the 36 extended abstracts selected for oral presentation at RE-
COMB 2015 by the Program Committee (PC) out of 170 submissions. Each submission
was assigned to at least three PC members and reviewed with the help of many exter-
nal reviewers. Following the initial reviews, there was an extensive discussion of the
submissions among the members of the PC, leading to the final decisions.
In 2015 RECOMB allowed for parallel submissions to the proceedings and a jour-
nal. Papers accepted for oral presentation that have simultaneously been submitted to a
journal are published as 2-page abstracts. Parallel submissions which have not appeared
in a journal by the time of the conference were to be deposited in the preprint server
arxiv.org. All other papers that were accepted to RECOMB 2015 were invited for sub-
mission in an edited journal version to a special issue of the Journal of Computational
Biology.
In addition to the paper presentations, RECOMB 2015 featured six invited keynote
talks by leading scientists world-wide. The keynote speakers were M. Madan Babu
(MRC Laboratory of Molecular Biology), Bonnie Berger (Broad Institute of Harvard
and MIT), M. Magda Konarska (Rockefeller University and University of Warsaw),
Michael Levitt (Stanford University), Bas van Steensel (Netherlands Cancer Institute),
and Ulam’s lecture by Waclaw Szybalski (University of Wisconsin-Madison).
Following the tradition started at RECOMB 2010, RECOMB 2015 also featured a
special highlights track containing computational biology papers that were published
in journals during the last 18 months. There were 38 submissions, 8 of which were
selected for oral presentation.
The success of RECOMB depends on the effort, dedication, and devotion of many
colleagues who have contributed to the organization of the conference. I thank the PC
members and external reviewers for the timely review of the assigned papers despite
their busy schedules; Mona Singh for chairing the highlights track; Lenore Cowen for
chairing the posters track; the Steering Committee and its chair, Martin Vingron, for
many excellent suggestions on the organization of the conference; the Local Organiz-
ing Committee members, especially the Co-chairs Jerzy Tiuryn and Bartek Wilczyński,
for hosting the conference and providing administrative, logistic, and financial sup-
port; and the authors of the papers, highlights, and posters and all the attendees for
their enthusiastic participation in the conference. We also thank our generous sponsors,
including the International Society of Computational Biology (ISCB), the US National
VI Preface

Science Foundation, the Polish Ministry of Science and Education, the Warsaw Center
for Mathematics and Computer Science, the Polish Bioinformatics Society, the Univer-
sity of Pittsburgh, and Biogen Idec. Finally, I would like to thank Roded Sharan (Tel
Aviv University; Program Chair of RECOMB 2014) for his support and advice.

February 2015 Teresa M. Przytycka

 Organization

Program Committee
Tatsuya Akutsu Kyoto University, Japan
Peter Arndt Max Planck Institute for Molecular Genetics,
Germany
Rolf Backofen University of Freiburg, Germany
Joel Bader Johns Hopkins University, USA
Vineet Bafna University of California, San Diego, USA
Nuno Bandeira University of California, San Diego, USA
Ziv Bar-Joseph Carnegie Mellon University, USA
Serafim Batzoglou Stanford University, USA
Jan Baumbach University of Southern Denmark, Denmark
Niko Beerenwinkel ETH Zurich, Switzerland
Panayiotis Takis Benos University of Pittsburgh, USA
Bonnie Berger Massachusetts Institute of Technology, USA
Jadwiga Bienkowska Biogen Idec, USA
Mathieu Blanchette McGill University, Canada
Jacek Błażewicz Poznań University of Technology, Poland
Michael R. Brent Washington University, St. Louis, USA
Chakra Chennubhotla University of Pittsburgh, USA
Lenore J. Cowen Tufts University, USA (Poster Chair)
Colin Dewey University of Wisconsin-Madison, USA
Dannie Durand Carnegie Mellon University, USA
Nadia El-Mabrouk Université de Montréal, Canada
Julien Gagneur Ludwig-Maximilians-Universität München,
Germany
Anna Gambin University of Warsaw, Poland
Irit Gat-Viks Tel Aviv University, Israel
Mikhail Gelfand Russian Academy of Sciences, Russia
David Gifford Massachusetts Institute of Technology, USA
Anna Goldenberg University of Toronto, Canada
Eran Halperin International Computer Science Institute, USA
Alexander Hartemink Duke University, USA
Michael Hoffman University of Toronto, Canada
Trey Ideker University of California, San Diego, USA
VIII Organization

Sorin Istrail Brown University, USA

Tao Jiang University of California, Riverside, USA
Igor Jurisica Ontario Cancer Institute, Canada
Tamer Kahveci University of Florida, USA
Simon Kasif Boston University, USA
Carl Kingsford Carnegie Mellon University, USA
Mehmet Koyuturk Case Western Reserve University, USA
Rui Kuang University of Minnesota Twin Cities, USA
Jens Lagergren KTH Royal Institute of Technology, Sweden
Thomas Lengauer Max Planck Institute for Informatics, Germany
Christina Leslie Memorial Sloan Kettering Cancer Center, USA
Michal Linial The Hebrew University of Jerusalem, Israel
Stefano Lonardi University of California, Riverside, USA
Paul Medvedev Pennsylvania State University, USA
Tijana Milenkovic University of Notre Dame, USA
Satoru Miyano University of Tokyo, Japan
Bernard Moret École Polytechnique Fédérale de Lausanne,
Switzerland
Chad Myers University of Minnesota, Twin Cities, USA
William Stafford Noble University of Washington, USA
Laxmi Parida IBM T.J. Watson Research Center, USA
Dana Pe’er Columbia Univeristy, USA
Jian Peng University of Illinois at Urbana-Champaign, USA
Mihai Pop University of Maryland, USA
Teresa Przytycka National Institutes of Health, USA (Chair)
Ben Raphael Brown University, USA
Knut Reinert Freie Universität Berlin, Germany
Maga Rowicka University of Texas Medical Branch, USA
Marie-France Sagot Inria, France
Cenk Sahinalp Indiana University, USA
David Sankoff University of Ottawa, Canada
Russell Schwartz Carnegie Mellon University, USA
Roded Sharan Tel Aviv University, Israel
Mona Singh Princeton University, USA (Highlights Chair)
Donna Slonim Tufts University, USA
Fengzhu Sun University of Southern California, USA
Glenn Tesler University of California, San Diego, USA
Jerzy Tiuryn University of Warsaw, Poland
Alfonso Valencia Spanish National Cancer Research Centre, Spain
Fabio Vandin University of Southern Denmark, Denmark
Martin Vingron Max Planck Institute for Molecular Genetics,
Germany
Jerome Waldispuhl McGill University, Canada
Esti Yeger-Lotem Ben-Gurion University of the Negev, Israel
Michal Ziv-Ukelson Ben-Gurion University of the Negev, Israel
 Organization IX

Steering Committee
Vineet Bafna University of California, San Diego, USA
Serafim Batzoglou Stanford University, USA
Bonnie Berger Massachusetts Institute of Technology, USA
Sorin Istrail Brown University, USA
Michal Linial The Hebrew University of Jerusalem, Israel
Martin Vingron Max Planck Institute for Molecular Genetics,
Germany (Chair)

Organizing Committee
Paweł Bednarz University of Warsaw, Poland
Agata Charzyńska Polish Academy of Sciences, Poland
Norbert Dojer University of Warsaw, Poland
Anna Gambin University of Warsaw, Poland
Paweł Górecki University of Warsaw, Poland
Aleksander Jankowski University of Warsaw, Poland
Agnieszka Mykowiecka University of Warsaw, Poland
Jerzy Tiuryn University of Warsaw, Poland (Co-chair)
Irina Tuszyńska International Institute of Molecular and
Cell Biology, Poland
Bartek Wilczyński University of Warsaw, Poland (Co-chair)
Damian Wójtowicz National Institutes of Health, USA
Rafał Zaborowski University of Warsaw, Poland
X Organization

Previous RECOMB Meetings

Dates Hosting Institution Program Chair Conference Chair
January 20-23, 1997 Sandia National Lab Michael Waterman Sorin Istrail
Santa Fe, NM, USA
March 22-25, 1998 Mt. Sinai School of Medicine Pavel Pevzner Gary Benson
New York, NY, USA
April 22-25, 1999 Inria Sorin Istrail Mireille Regnier
Lyon, France
April 8-11, 2000 University of Tokyo Ron Shamir Satoru Miyano
Tokyo, Japan
April 22-25, 2001 Université de Montréal Thomas Lengauer David Sankoff
Montréal, Canada
April 18-21, 2002 Celera Gene Myers Sridhar
Washington, DC, USA Hannenhalli
April 10-13, 2003 German Federal Ministry for Webb Miller Martin Vingron
Berlin, Germany Education and Research
March 27-31, 2004 University of California, Dan Gusfield Philip E. Bourne
San Diego, USA San Diego
May 14-18, 2005 Broad Institute of MIT and Satoru Miyano Jill P. Mesirov and
Boston, MA, USA Harvard Simon Kasif
April 2-5, 2006 University of Padua Alberto Apostolico Concettina Guerra
Venice, Italy
April 21-25, 2007 QB3 Terry Speed Sandrine Dudoit
San Francisco, CA, USA
March 30-April 2, 2008 National University of Martin Vingron Limsoon Wong
Singapore, Singapore Singapore
May 18-21, 2009 University of Arizona Serafim Batzoglou John Kececioglu
Tucson, AZ, USA
August 12-15, 2010 INESC-ID and Instituto Bonnie Berger Arlindo Oliveira
Lisbon, Portugal Superior Técnico
March 28-31, 2011 Lab for Computational Biology, Vineet Bafna S. Cenk Sahinalp
Vancouver, Canada Simon Fraser University
April 21-24, 2012 Centre for Genomic Regulation Benny Chor Roderic Guigó
Barcelona, Spain
April 7-10, 2013 Tsinghua University Fengzhu Sun Xuegong Zhang
Beijing, China
April 2-5, 2014 Carnegie Mellon University and Roded Sharan Russell Schwartz and
Pittsburgh, PA, USA University of Pittsburgh Panayiotis (Takis) Benos

External Reviewers
Aguiar, Derek Ay, Ferhat
Ahmed, Bilal Ayati, Marzieh
Ahmed, Hazem Azizi, Elham
Akey, Joshua Barbosa, Eudes
Albrecht, Mario Batra, Richa
Alekseyev, Max Becerra, David
Alhakami, Hind Behr, Jonas
Almeida, Mathieu Bernstein, Laurence
Antczak, Maciej Bhasin, Jeffrey
Arvestad, Lars Bishara, Alex
Atias, Nir Blumer, Anselm
 Organization XI

Botzman, Maya Harel, Tom

Bozdag, Serdar Hasan, Abid
Can, Tolga Hasan, Mahmudul
Cao, Mengfei Haspel, Nurit
Carmel, Amir Hauschild, Anne-Christin
Carty, Mark Hauswedell, Hannes
Chen, Quan He, Dan
Chen, Brian Heinig, Matthias
Chicco, Davide Heringa, Jaap
Chikhi, Rayan Hescott, Benjamin
Cho, Dongyeon Hill, Christopher
Cicek, A. Ercument Hodzic, Ermin
Constantinescu, Simona Hoener Zu Siederdissen, Christian
Daniels, Noah Hoffmann, Steve
Dao, Phuong Hofree, Matan
Darby, Charlotte Hoinka, Jan
Davidson, Philip Holtby, Daniel
Davydov, Iakov Hormozdiari, Fereydoun
Dimitrakopoulos, Christos Hosur, Raghavendra
Dojer, Norbert Huang, Lin
Donald, Bruce Huska, Matt
Donmez, Nilgun Iersel van, Leo
Dutkowski, Janusz Irannia, Zohreh Baharvand
Edwards, Matthew Jain, Siddhartha
El-Kebir, Mohammed Jensen, James
Elhesha, Rasha Kalinina, Olga
Filippova, Darya Kayano, Mitsunori
Flamm, Christoph Keasar, Chen
Frånberg, Mattias Keich, Uri
Frellsen, Jes Kierzynka, Michal
Frishberg, Amit Koch, Elizabeth
Gabr, Haitham Kohlbacher, Oliver
Gartzman, Dalya Kolodny, Rachel
Gendoo, Deena Kramer, Michael
Gitter, Anthony Krishnaswamy, Smita
Golumbeanu, Monica Kuipers, Jack
Gonzalez, Alvaro Łacki,
˛ Mateusz Krzysztof
Górecki, Paweł Lafond, Manuel
Guo, Yuchun Lai, Han
Guthals, Adrian Lajoie, Mathieu
Haas, Brian Lang, Brian
Hach, Faraz Lange, Sita
Haiminen, Niina Laukens, Kris
Hajirasouliha, Iman Li, Wenyuan
Halldorsson, Bjarni Liang, Xiao
Hamel, Sylvie Liao, Chung-Shou
XII Organization

Libbrecht, Max Platts, Adrian

Lin, Yen Yi Polishko, Anton
Lindner, Martin S. Pons, Carles
Linz, Simone Popic, Victoria
List, Markus Prabhakaran, Sandhya
Liu, Yuling Pritykin, Yuri
Love, Michael Przytycki, Pawel
Lu, Yuheng Radom, Marcin
Lu, Yong Rarey, Matthias
Lukasiak, Piotr Reimand, Juri
Luo, Qiang Reinharz, Vladimir
Ma, Wenxiu Ritz, Anna
Madej, Tom Roe, David
Maier, Ezekiel Rubinov, Anatoly
Malikic, Salem Rudolph, Jan
Mazza, Arnon Ruffalo, Matthew
Mcpherson, Andrew Sacomoto, Gustavo
Mezlini, Aziz Savel, Daniel
Mi, Huaiyu Schaefer, Rob
Mirebrahim, Seyed Hamid Sefer, Emre
Mironov, Andrey Sennblad, Bengt
Montazeri, Hesam Setty, Manu
Mosig, Axel Shao, Mingfu
Mueller, Jonas Sheinman, Misha
Muthiah, Senthil Shen, Yang
Mysickova, Alena Sheridan, Paul
Na, Seungjin Silverbush, Dana
Nachshon, Aharon Sindi, Suzanne
Nadimpalli, Shilpa Singh, Irtisha
Navlakha, Saket Skola, Dylan
Nelson, Justin Smaoui, Mohamed
Niida, Atsushi Solomon, Brad
Numanagic, Ibrahim Startek, Michał
Oesper, Layla Steuerman, Yael
Ofer, Dan Syed, Tahin
Ounit, Rachid Todor, Andrei
Pan, Weihua Tofigh, Ali
Park, Heewon Tomescu, Alexandru I.
Paulson, Joseph Tremblay-Savard, Olivier
Persikov, Anton Vandersluis, Benjamin
Pervouchine, Dmitri Veksler-Lublinsky, Isana
Pfeifer, Nico Vert, Jean-Philippe
Pfeuffer, Julianus Viner, Coby
Pham, Son Vinga, Susana
Pisanti, Nadia Walevski, Uri
Plat, Daniel Wan, Lin
 Organization XIII

Wang, Bo Yavas, Gokhan

Wang, Wen Yoo-Ah, Kim
Wang, Sheng You, Xintian
Wang, Jie Yu, Mike
Wang, Mingxun Yuan, Han
Wang, Jian Zakov, Shay
Wang, Mingxun Zamalloa, Jose
Wise, Aaron Zhang, Wei
Wiwie, Christian Zhang, Huanan
Wojciechowski, Pawel Zhang, Yao-Zhong
Wolfson, Haim Zheng, Jie
Wu, Xuebing Zhong, Shan
Yang, Li Zirbel, Craig
 Contents

Efficient Alignment Free Sequence Comparison with Bounded Mismatches . . . 1

Srinivas Aluru, Alberto Apostolico, and Sharma V. Thankachan

DockStar: A Novel ILP Based Integrative Method for Structural Modelling

of Multimolecular Protein Complexes (Extended Abstract) . . . . . . . . . . . . . 13
Naama Amir, Dan Cohen, and Haim J. Wolfson

CRISPR Detection from Short Reads Using Partial Overlap Graphs . . . . . . . 16

Ilan Ben-Bassat and Benny Chor

HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction

from Transcriptome and Genome Sequencing Data. . . . . . . . . . . . . . . . . . . 28
Emily Berger, Deniz Yorukoglu, and Bonnie Berger

Read Clouds Uncover Variation in Complex Regions

of the Human Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Alex Bishara, Yuling Liu, Dorna Kashef-Haghighi, Ziming Weng,
Daniel E. Newburger, Robert West, Arend Sidow, and Serafim Batzoglou

Learning Microbial Interaction Networks from Metagenomic Count Data . . . 32

Surojit Biswas, Meredith McDonald, Derek S. Lundberg, Jeffery L. Dangl,
and Vladimir Jojic

Immunoglobulin Classification Using the Colored Antibody Graph. . . . . . . . 44

Stefano R. Bonissone and Pavel A. Pevzner

CIDANE: Comprehensive Isoform Discovery and Abundance Estimation . . . 60

Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert,
and Gunnar W. Klau

Diffusion Component Analysis: Unraveling Functional Topology

in Biological Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Hyunghoon Cho, Bonnie Berger, and Jian Peng

Fragmentation Trees Reloaded . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Kai Dührkop and Sebastian Böcker

KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids . . . . . . 80

Rasmus Fonseca, Henry van den Bedem, and Julie Bernauer

Locating a Tree in a Phylogenetic Network in Quadratic Time . . . . . . . . . . 96

Philippe Gambette, Andreas D.M. Gunawan, Anthony Labarre,
Stéphane Vialette, and Louxin Zhang
XVI Contents

Constructing Structure Ensembles of Intrinsically Disordered Proteins

from Chemical Shift Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong,
and Jianyang Zeng

COMETS (Constrained Optimization of Multistate Energies by Tree Search):

A Provable and Efficient Algorithm to Optimize Binding Affinity
and Specificity with Respect to Sequence . . . . . . . . . . . . . . . . . . . . . . . . . 122
Mark A. Hallen and Bruce R. Donald

Efficient and Accurate Multiple-Phenotypes Regression Method

for High Dimensional Data Considering Population Structure . . . . . . . . . . . 136
Jong Wha J. Joo, Eun Yong Kang, Elin Org, Nick Furlotte, Brian Parks,
Aldons J. Lusis, and Eleazar Eskin

BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming

Algorithm for Sparse Approximations of Computational Protein Design . . . . 154
Jonathan D. Jou, Swati Jain, Ivelin Georgiev, and Bruce R. Donald

An Efficient Nonlinear Regression Approach for Genome-wide Detection

of Marginal and Interacting Genetic Variations . . . . . . . . . . . . . . . . . . . . . 167
Seunghak Lee, Aurélie Lozano, Prabhanjan Kambadur, and Eric P. Xing

Exploration of Designability of Proteins Using Graph Features

of Contact Maps: Beyond Lattice Models . . . . . . . . . . . . . . . . . . . . . . . . . 188
Sumudu P. Leelananda, Robert L. Jernigan, and Andrzej Kloczkowski

CoMEt: A Statistical Approach to Identify Combinations of Mutually

Exclusive Alterations in Cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
Mark D.M. Leiserson, Hsin-Ta Wu, Fabio Vandin, and Benjamin J. Raphael

Deep Feature Selection: Theory and Application to Identify Enhancers

and Promoters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Yifeng Li, Chih-Yu Chen, and Wyeth W. Wasserman

Protein Contact Prediction by Integrating Joint Evolutionary Coupling

Analysis and Supervised Learning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
Jianzhu Ma, Sheng Wang, Zhiyong Wang, and Jinbo Xu

ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching . . . 222

Igor Mandric and Alex Zelikovsky

A Symmetric Length-Aware Enrichment Test . . . . . . . . . . . . . . . . . . . . . . 224

David Manescu and Uri Keich

Functional Alignment of Metabolic Networks . . . . . . . . . . . . . . . . . . . . . . 243

Arnon Mazza, Allon Wagner, Eytan Ruppin, and Roded Sharan
 Efficient Alignment Free Sequence Comparison with Bounded Mismatches 11

6 Conclusions
We present an efficient algorithm for the k-mismatch average common substring
problem that runs in O(n logk+1 n) time and O(n) space. This constitutes a
significant improvement over the O(n2 ) worst case run-time of the prior state
of the art. In the absence of the proposed space-saving technique, our algorithm
would have taken O(n logk n) space, which would be impractical for even small
values of k. Our algorithm achieves linear working space by decomposing the set
of modified suffixes so that they can be processed and discarded independently,
while preserving the ability to bring pairs of modified suffixes together. Note
that the biological applications of ACSk are well documented in [14]. The vastly
improved efficiency in computing ACSk by our algorithm should naturally impact
these applications positively.

Acknowledgments. This research is supported in part by the U.S. National Science

Foundation under CCF-1360593 and IIS-1416259.

A Ordering of Pairs
Consider three strings in B2 and their associated modifications.

1. str1 = AGT GT and {(2, G), (3, T )},

2. str2 = T ACCG and {(2, A), (4, C)},
3. str3 = T GCAA and {(1, T ), (4, A)}.

Then the list of elements in P2 are in the following order.

– ({}, str1 )
– ({}, str2 )
– ({}, str3 )

– ({(1, T )}, str3 )

– ({(2, G)}, str1 )
– ({(2, A)}, str2 )
– ({(3, T )}, str1 )
– ({(4, C)}, str2 )
– ({(4, A)}, str3 )

– ({(1, T ), (4, A)}, str3 )

– ({(2, G), (3, T )}, str1 )
– ({(2, A), (4, C)}, str2 )
12 S. Aluru et al.

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