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Methods in
Molecular Biology 1757
Martin Kollmar Editor
Eukaryotic
Genomic
Databases
Methods and Protocols
Methods in Molecular Biology
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes:

http://www.springer.com/series/7651
Eukaryotic Genomic Databases
Methods and Protocols
Edited by
Martin Kollmar
Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology,
Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
Editor
Martin Kollmar
Group Systems Biology of Motor Proteins
Department of NMR-Based Structural Biology
Max-Planck-Institute for Biophysical Chemistry
Göttingen, Germany
ISSN 1064-3745 ISSN 1940-6029 (electronic)

Methods in Molecular Biology
ISBN 978-1-4939-7736-9 ISBN 978-1-4939-7737-6 (eBook)
https://doi.org/10.1007/978-1-4939-7737-6
Library of Congress Control Number: 2018935916
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Preface
Since genome sequencing became affordable, the number of available eukaryotic genomes
has dramatically increased. Large-scale sequencing of thousands of species is under way
(e.g., 1k fungi project, Y1000+ yeast project, Genomes 10k vertebrates project, B10K bird
project, 5k insects project, 959 nematodes project, 10KP plant project). Species-dedicated
communities complement genome-based knowledge by population genomics, transcrip-
tomics, and various other types of data. This volume introduces databases containing
genome-based data and providing access to genome-wide analyses. The primary audience
involves geneticists and molecular biologists who want to keep their knowledge up to date
on where and how to obtain eukaryotic genomics data. Many databases also contain more
complex data and analyses that are often hidden to the novice or occasional user and are
usually not described in documentations or online help pages. Chapters will describe data-
base contents as well as typical use cases, written in the spirit of the series which aims to
provide practical guidance and troubleshooting advice. The focus of this book is on data-
bases from all taxa except plants, which are described in another volume.
Although most of the databases provide access to the same data analysis tools such as
BLAST, JBrowse, and InterMine, and connect the genome annotations with the same fea-
ture databases such as GO, KEGG, Pfam, and phenotype ontologies, the described use
cases and approaches to capture and combine these data are very different. Therefore, it is
highly recommended to read and follow the protocols of multiple chapters even if the main
interest is in a single species or taxon. The databases presented in this volume are under
active curation and development. General technological developments and demands to
integrate extended and new data types will lead to continuous changes to and major updates
of these databases. However, the rationale how to access and combine the described
genomic data will remain independent of whether the look and feel of tools will change.
The clear guidance presented in the chapters should facilitate accessing eukaryotic genomic
data and stimulate comparative genomic research.
Göttingen, Germany Martin Kollmar
v
Acknowledgment
Pedro Assis, Gail Binkley, Juan Carlos Chan, J. Michael Cherry, Anne Eagle, Ken Frazer,
Sibyl Gao, Patrick Kalita, Kalpana Karra, Jonathan Knight, Ruben Lancaster, Kevin
MacPherson, Prita Mani, Ryan Martin, Stuart Miyasato, Sierra Moxon, Hans-Michael
Muller, Cecilia Nakamura, Paulo Nuin, Holly Paddock, Christian Pich, Matthew Russell,
Kevin Schaper, Tim Schedl, Gary Schindelman, Xiang Shao, Travis Sheppard, Matt Simison,
Amy Singer, Lincoln Stein, Paul W. Sternberg, Sabrina Toro, Daniel Wang, Shuai Weng,
Edith Wong, Adam Wright, Karen Yook
vii
Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Acknowledgment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 Identifying Sequenced Eukaryotic Genomes and Transcriptomes

with diArk�� 1
Martin Kollmar and Dominic Simm
2 An Introduction to the Saccharomyces Genome Database (SGD) �� 21
Olivia W. Lang, Robert S. Nash, Sage T. Hellerstedt, Stacia R. Engel,
and The SGD Project
3 Using the Candida Genome Database�� 31
Marek S. Skrzypek, Jonathan Binkley, and Gavin Sherlock
4 PomBase: The Scientific Resource for Fission Yeast �� 49
Antonia Lock, Kim Rutherford, Midori A. Harris, and Valerie Wood
5 EuPathDB: The Eukaryotic Pathogen Genomics Database Resource�� 69
Susanne Warrenfeltz, Evelina Y. Basenko, Kathryn Crouch, Omar S. Harb,
Jessica C. Kissinger, David S. Roos, Achchuthan Shanmugasundram,
and Fatima Silva-Franco
6 The Ensembl Genome Browser: Strategies for Accessing Eukaryotic
Genome Data �� 115
Victoria Newman, Benjamin Moore, Helen Sparrow, and Emily Perry
7 Mouse Genome Informatics (MGI) Is the International Resource
for Information on the Laboratory Mouse�� 141
MeiYee Law and David R. Shaw
8 A Primer for the Rat Genome Database (RGD)�� 163
Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang,
Jennifer R. Smith, Victoria Petri, Matthew J. Hoffman, Jeff De Pons,
Marek A. Tutaj, Omid Ghiasvand, Monika Tutaj, Jyothi Thota,
Melinda R. Dwinell, and Mary Shimoyama
9 Bovine Genome Database: Tools for Mining the Bos taurus Genome�� 211
Darren E. Hagen, Deepak R. Unni, Aditi Tayal, Gregory W. Burns,
and Christine G. Elsik
10 Navigating Xenbase: An Integrated Xenopus Genomics and Gene
Expression Database �� 251
Christina James-Zorn, Virgilio Ponferrada, Malcolm E. Fisher,
Kevin Burns, Joshua Fortriede, Erik Segerdell, Kamran Karimi,
Vaneet Lotay, Dong Zhuo Wang, Stanley Chu, Troy Pells, Ying Wang,
Peter D. Vize, and Aaron Zorn
11 Using ZFIN: Data Types, Organization, and Retrieval�� 307
Ceri E. Van Slyke, Yvonne M. Bradford, Douglas G. Howe, David S. Fashena,
Sridhar Ramachandran, Leyla Ruzicka, and ZFIN Staff
ix
x Contents
12 EchinoBase: Tools for Echinoderm Genome Analyses �� 349

Gregory A. Cary, R. Andrew Cameron, and Veronica F. Hinman
13 A Multi-Omics Database for Parasitic Nematodes and Trematodes�� 371
John Martin, Rahul Tyagi, Bruce A. Rosa, and Makedonka Mitreva
14 Using WormBase: A Genome Biology Resource
for Caenorhabditis elegans and Related Nematodes�� 399
Christian Grove, Scott Cain, Wen J. Chen, Paul Davis, Todd Harris,
Kevin L. Howe, Ranjana Kishore, Raymond Lee, Michael Paulini,
Daniela Raciti, Mary Ann Tuli, Kimberly Van Auken, Gary Williams,
and The WormBase Consortium
15 Using WormBase ParaSite: An Integrated Platform for Exploring
Helminth Genomic Data�� 471
Bruce J. Bolt, Faye H. Rodgers, Myriam Shafie, Paul J. Kersey, Matthew
Berriman, and Kevin L. Howe
16 Using FlyBase to Find Functionally Related Drosophila Genes �� 493
Alix J. Rey, Helen Attrill, Steven J. Marygold, and The FlyBase Consortium
17 Hymenoptera Genome Database: Using HymenopteraMine to Enhance
Genomic Studies of Hymenopteran Insects �� 513
Christine G. Elsik, Aditi Tayal, Deepak R. Unni, Gregory W. Burns,
and Darren E. Hagen
18 Navigating the i5k Workspace@NAL: A Resource for Arthropod Genomes�� 557
Monica F. Poelchau, Mei-Ju May Chen, Yu-Yu Lin,
and Christopher P. Childers
Index�� 579
Contributors
Julie Agapite · Biological Laboratories, Harvard University, Cambridge, MA, USA

Giulia Antonazzo · Department of Physiology, Development and Neuroscience,
University of Cambridge, Cambridge, UK
Helen Attrill · Department of Physiology, Development and Neuroscience, University of
Cambridge, Cambridge, UK
Kimberly Van Auken · Division of Biology and Biological Engineering, California
Institute of Technology, Pasadena, CA, USA
Phillip Baker · Department of Biology, University of New Mexico, Albuquerque, NM,
USA
Evelina Y. Basenko · Centre for Genomic Research, Institute of Integrative Biology,
University of Liverpool, Liverpool, UK
Matthew Berriman · Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Jonathan Binkley · Department of Genetics, Stanford University, Stanford, CA, USA
Bruce J. Bolt · European Molecular Biology Laboratory, European Bioinformatics
Institute (EMBL-EBI), Hinxton, Cambridge, UK
Yvonne M. Bradford · The Zebrafish Information Network, University of Oregon,
Eugene, OR, USA
Kris Broll · Biological Laboratories, Harvard University, Cambridge, MA, USA
Nicholas Brown · Department of Physiology, Development and Neuroscience, University
of Cambridge, Cambridge, UK
Gregory W. Burns · Division of Animal Sciences, University of Missouri, Columbia,
MO, USA
Kevin Burns · Xenbase Curation Team, Division of Developmental Biology, Cincinnati
Children’s Hospital, Cincinnati, OH, USA
Scott Cain · Informatics and Bio-computing Platform, Ontario Institute for Cancer
Research, Toronto, ON, Canada
R. Andrew Cameron · Department of Biological Sciences, Mellon Institute, Carnegie
Mellon University, Pittsburgh, PA, USA; Division of Biology and Biological Engineering,
California Institute of Technology, Pasadena, CA, USA
Gregory A. Cary · Department of Biological Sciences, Mellon Institute, Carnegie Mellon
University, Pittsburgh, PA, USA
Mei-Ju May Chen · Graduate Institute of Biomedical Electronics and Bioinformatics,
National Taiwan University, Taipei, Taiwan
Wen J. Chen · Division of Biology and Biological Engineering, California Institute of
Technology, Pasadena, CA, USA
Christopher P. Childers · USDA, Agricultural Research Service, National Agricultural
Library, Beltsville, MD, USA
Stanley Chu · Xenbase Development Team, Department of Computer Science, University
of Calgary, Calgary, AB, Canada; Xenbase Development Team, Department of
Biological Science, University of Calgary, Calgary, AB, Canada
Richard Cripps · Department of Biology, University of New Mexico, Albuquerque,
NM, USA
xi
xii Contributors
Madeline Crosby · Biological Laboratories, Harvard University, Cambridge, MA, USA

Kathryn Crouch · Wellcome Trust Centre for Molecular Parasitology, University of
Glasgow, Glasgow, UK
Bryon Czoch · Department of Biology, Indiana University, Bloomington, IN, USA
Paul Davis · European Molecular Biology Laboratory, European Bioinformatics Institute,
Cambridge, UK
Melinda R. Dwinell · Genomic Sciences and Precision Medicine Center, Medical College
of Wisconsin, Milwaukee, WI, USA; Department of Physiology, Medical College of
Wisconsin, Milwaukee, WI, USA
Christine G. Elsik · Division of Animal Sciences, University of Missouri, Columbia,
MO, USA; Division of Plant Sciences, University of Missouri, Columbia, MO, USA;
MU Informatics Institute, University of Missouri, Columbia, MO, USA
David Emmert · Biological Laboratories, Harvard University, Cambridge, MA, USA
Stacia R. Engel · Department of Genetics, Stanford University, Palo Alto, CA, USA
Kathleen Falls · Biological Laboratories, Harvard University, Cambridge, MA, USA
David S. Fashena · The Zebrafish Information Network, University of Oregon, Eugene,
OR, USA
Silvie Fexova · Department of Physiology, Development and Neuroscience, University of
Malcolm E. Fisher · Xenbase Curation Team, Division of Developmental Biology,
Cincinnati Children’s Hospital, Cincinnati, OH, USA
Joshua Fortriede · Xenbase Curation Team, Division of Developmental Biology,
Phani Garapati · Department of Physiology, Development and Neuroscience, University of
Susan Russo Gelbart · Biological Laboratories, Harvard University, Cambridge,
MA, USA
Omid Ghiasvand · Department of Biomedical Engineering, Medical College of Wisconsin
and Marquette University, Milwaukee, WI, USA
Josh Goodman · Department of Biology, Indiana University, Bloomington, IN, USA
Sian Gramates · Biological Laboratories, Harvard University, Cambridge, MA, USA
Christian Grove · Division of Biology and Biological Engineering, California Institute of
Gary Grumbling · Department of Biology, Indiana University, Bloomington, IN, USA
Darren E. Hagen · Division of Animal Sciences, University of Missouri, Columbia,
MO, USA
Omar S. Harb · Department of Biology, University of Pennsylvania, Philadelphia,
PA, USA
Midori A. Harris · Department of Biochemistry, Cambridge Systems Biology Centre,
Todd Harris · Informatics and Bio-computing Platform, Ontario Institute for Cancer
Research, Toronto, ON, Canada
G. Thomas Hayman · Department of Biomedical Engineering, Medical College of
Wisconsin and Marquette University, Milwaukee, WI, USA
Sage T. Hellerstedt · Department of Genetics, Stanford University, Palo Alto, CA, USA
Veronica F. Hinman · Department of Biological Sciences, Mellon Institute, Carnegie
Mellon University, Pittsburgh, PA, USA
Contributors xiii
Matthew J. Hoffman · Genomic Sciences and Precision Medicine Center, Medical College
of Wisconsin, Milwaukee, WI, USA; Department of Physiology, Medical College of
Wisconsin, Milwaukee, WI, USA
Douglas G. Howe · The Zebrafish Information Network, University of Oregon, Eugene,
OR, USA
Kevin L. Howe · European Molecular Biology Laboratory, European Bioinformatics
Christina James-Zorn · Xenbase Curation Team, Division of Developmental Biology,
Tamsin Jones · Department of Physiology, Development and Neuroscience, University of
Kamran Karimi · Xenbase Development Team, Department of Computer Science,
University of Calgary, Calgary, AB, Canada; Xenbase Development Team, Department
of Biological Science, University of Calgary, Calgary, AB, Canada
Thomas Kaufman · Department of Biology, Indiana University, Bloomington, IN, USA
Paul J. Kersey · European Molecular Biology Laboratory, European Bioinformatics
Ranjana Kishore · Division of Biology and Biological Engineering, California Institute of
Jessica C. Kissinger · Center for Tropical and Emerging Global Diseases, University of
Georgia, Athens, GA, USA; Institute of Bioinformatics, University of Georgia, Athens,
GA, USA; Department of Genetics, University of Georgia, Athens, GA, USA
Martin Kollmar · Group Systems Biology of Motor Proteins, Department of NMR-Based
Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
Olivia W. Lang · Department of Genetics, Stanford University, Palo Alto, CA, USA
Aoife Larkin · Department of Physiology, Development and Neuroscience, University of
Stanley J. F. Laulederkind · Department of Biomedical Engineering, Medical College of
Wisconsin and Marquette University, Milwaukee, WI, USA
MeiYee Law · Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA
Raymond Lee · Division of Biology and Biological Engineering, California Institute of
Yu-Yu Lin · Graduate Institute of Biomedical Electronics and Bioinformatics, National
Taiwan University, Taipei, Taiwan
Antonia Lock · Department of Genetics, Evolution and Environment, University College
London, London, UK
Vaneet Lotay · Xenbase Development Team, Department of Computer Science, University
of Calgary, Calgary, AB, Canada; Xenbase Development Team, Department of
Biological Science, University of Calgary, Calgary, AB, Canada
John Martin · McDonnell Genome Institute, Washington University in St. Louis, St.
Louis, MO, USA
Steven J. Marygold · Department of Physiology, Development and Neuroscience,
Beverley Matthews · Biological Laboratories, Harvard University, Cambridge, MA,
USA
Gillian Millburn · Department of Physiology, Development and Neuroscience, University
of Cambridge, Cambridge, UK
xiv Contributors
Makedonka Mitreva · McDonnell Genome Institute, Washington University in St. Louis,

St. Louis, MO, USA; Division of Infectious Diseases, Department of Medicine,
Washington University School of Medicine, St. Louis, MO, USA
Benjamin Moore · European Molecular Biology Laboratory, European Bioinformatics
Institute, Cambridge, UK
Robert S. Nash · Department of Genetics, Stanford University, Palo Alto, CA, USA
Victoria Newman · European Molecular Biology Laboratory, European Bioinformatics
Michael Paulini · European Molecular Biology Laboratory, European Bioinformatics
Troy Pells · Xenbase Development Team, Department of Computer Science, University of
Calgary, Calgary, AB, Canada; Xenbase Development Team, Department of Biological
Science, University of Calgary, Calgary, AB, Canada
Norbert Perrimon · Biological Laboratories, Harvard University, Cambridge, MA, USA
Emily Perry · European Molecular Biology Laboratory, European Bioinformatics Institute,
Cambridge, UK
Victoria Petri · Department of Biomedical Engineering, Medical College of Wisconsin
Monica F. Poelchau · USDA, Agricultural Research Service, National Agricultural
Library, Beltsville, MD, USA
Virgilio Ponferrada · Xenbase Curation Team, Division of Developmental Biology,
Jeff De Pons · Department of Biomedical Engineering, Medical College of Wisconsin and
Marquette University, Milwaukee, WI, USA
Daniela Raciti · Division of Biology and Biological Engineering, California Institute of
Sridhar Ramachandran · The Zebrafish Information Network, University of Oregon,
Eugene, OR, USA
Alix J. Rey · Department of Physiology, Development and Neuroscience, University of
Faye H. Rodgers · Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
David S. Roos · Department of Biology, University of Pennsylvania, Philadelphia, PA,
USA
Bruce A. Rosa · McDonnell Genome Institute, Washington University in St. Louis,
St. Louis, MO, USA
Kim Rutherford · Department of Biochemistry, Cambridge Systems Biology Centre,
Leyla Ruzicka · The Zebrafish Information Network, University of Oregon, Eugene, OR,
USA
Gilberto dos Santos · Biological Laboratories, Harvard University, Cambridge, MA,
USA
Erik Segerdell · Xenbase Curation Team, Division of Developmental Biology, Cincinnati
Myriam Shafie · Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Achchuthan Shanmugasundram · Centre for Genomic Research, Institute of Integrative
Biology, University of Liverpool, Liverpool, UK
Contributors xv
David R. Shaw · Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor,

ME, USA
Gavin Sherlock · Department of Genetics, Stanford University, Stanford, CA, USA
Mary Shimoyama · Department of Biomedical Engineering, Medical College of Wisconsin
Fatima Silva-Franco · Centre for Genomic Research, Institute of Integrative Biology,
University of Liverpool, Liverpool, UK
Dominic Simm · Group Systems Biology of Motor Proteins, Department of NMR-Based
Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany;
Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science,
Georg-August-University, Göttingen, Germany
Marek S. Skrzypek · Department of Genetics, Stanford University, Stanford, CA, USA
Ceri E. Van Slyke · The Zebrafish Information Network, University of Oregon, Eugene,
OR, USA
Jennifer R. Smith · Department of Biomedical Engineering, Medical College of Wisconsin
Helen Sparrow · European Molecular Biology Laboratory, European Bioinformatics
Victor Strelets · Department of Biology, Indiana University, Bloomington, IN, USA
Christopher Tabone · Biological Laboratories, Harvard University, Cambridge,
MA, USA
Aditi Tayal · Division of Animal Sciences, University of Missouri, Columbia, MO, USA
Jyothi Thota · Department of Biomedical Engineering, Medical College of Wisconsin and
Marquette University, Milwaukee, WI, USA
Jim Thurmond · Department of Biology, Indiana University, Bloomington, IN, USA
Vitor Trovisco · Department of Physiology, Development and Neuroscience,
Mary Ann Tuli · Division of Biology and Biological Engineering, California Institute of
Marek A. Tutaj · Department of Biomedical Engineering, Medical College of Wisconsin
Monika Tutaj · Department of Biomedical Engineering, Medical College of Wisconsin
Rahul Tyagi · McDonnell Genome Institute, Washington University in St. Louis, St. Louis,
MO, USA
Deepak R. Unni · Division of Animal Sciences, University of Missouri, Columbia,
MO, USA
Jose-Maria Urbano · Department of Physiology, Development and Neuroscience,
Peter D. Vize · Xenbase Development Team, Department of Computer Science, University
of Calgary, Calgary, AB, Canada
Dong Zhuo Wang · Xenbase Development Team, Department of Computer Science,
University of Calgary, Calgary, AB, Canada; Xenbase Development Team, Department
of Biological Science, University of Calgary, Calgary, AB, Canada
Shur-Jen Wang · Department of Biomedical Engineering, Medical College of Wisconsin
xvi Contributors
Ying Wang · Xenbase Development Team, Department of Computer Science, University of

Calgary, Calgary, AB, Canada; Xenbase Development Team, Department of Biological
Science, University of Calgary, Calgary, AB, Canada
Susanne Warrenfeltz · Center for Tropical and Emerging Global Diseases, University of
Georgia, Athens, GA, USA
Maggie Werner-Washburne · Department of Biology, University of New Mexico,
Albuquerque, NM, USA
Gary Williams · European Molecular Biology Laboratory, European Bioinformatics
Valerie Wood · Department of Biochemistry, Cambridge Systems Biology Centre,
Pinglei Zhou · Biological Laboratories, Harvard University, Cambridge, MA, USA
Aaron Zorn · Xenbase Curation Team, Division of Developmental Biology, Cincinnati
Mark Zytkovicz · Biological Laboratories, Harvard University, Cambridge, MA, USA
Chapter 1
Identifying Sequenced Eukaryotic Genomes

and Transcriptomes with diArk
Martin Kollmar and Dominic Simm
Abstract
The diArk Eukaryotic Genome Database is a manually curated and updated repository of available eukary-
otic genome and transcriptome assemblies. diArk is a key resource for researchers interested in comparative
eukaryotic genomics, and the entry point to browsing sequenced eukaryotes in general and to find the
most closely related species to the own organism of interest in particular. The exponentially increasing
number of sequenced species demands sophisticated search and data presentation tools. In this chapter we
describe how to navigate the diArk database keeping a first-time user in mind.
Key words Eukaryotes, Sequenced genomes, Genome assembly, Transcriptome assembly
1 Introduction
The diArk Eukaryotic Genome Database (http://www.diark.org)

was started in 2005 as a central repository for eukaryotes with
genome assembly data available [1]. The species comprised human,
the most widely used model organisms such as Drosophila melano-
gaster, Caenorhabditis elegans, and Arabidopsis thaliana, and mul-
tiple fungi. While dedicated databases were available for most of
these species connecting the genomes with additional data and
analyses, diArk filled the gap as central entry point allowing browsing
through the sequenced eukaryotome and providing links to species
databases and primary data repositories. Given the progress in
sequencing strategy and technology development it was clear that
genome assemblies will become available with increasing pace.
Several genome sequencing initiatives had been started aiming to
obtain genome assemblies of multiple related species. Large scale
at that time meant the sequencing of 12 Drosophila species [2] or
the sequencing of 29 low- and high-coverage mammalian genomes
[3]. Soon after, size and speed of the projects increased by two
Martin Kollmar (ed.), Eukaryotic Genomic Databases: Methods and Protocols, Methods in Molecular Biology, vol. 1757,
https://doi.org/10.1007/978-1-4939-7737-6_1, © Springer Science+Business Media, LLC, part of Springer Nature 2018
1
2 Martin Kollmar and Dominic Simm
orders of magnitude. Current large scale projects cover all major

branches of eukaryotic life and new genomes are released on a daily
basis. The most important ongoing whole-genome sequencing
projects are the sequencing of vertebrates within Genome 10K [4],
the sequencing of all 10,500 bird species within B10K [5], the
sequencing of 5,000 arthropods (i5k) [6], the 959 Nematodes
project [7, 8], the 1000 Fungal Genomes Project (1FKG;
http://1000.fungalgenomes.org), and the sequencing of 1000
yeasts (y1000+; https://y1000plus.wei.wisc.edu/). In addition,
transcriptomes have been sequenced and assembled from 1000
plants (1KP project) [9], more than 1200 insects (1KITE project;
http://www.1kite.org), and hundreds of marine microorganisms
within MMETSP (Marine Microbial Eukaryote Transcriptome
Sequencing Project) [10]. Pilot data have been obtained for two
further ambitious projects, the 1000 Plant & Animal Reference
Genomes Project and Fish-T1K [11], but it is not clear whether
these projects still continue. Most recently, plans to sequence the
genomes of at least 10,000 plants have been announced (10KP)
[12]. In addition to these massive sequencing efforts, there are
dozens of small-scale sequencing projects dedicated to a few spe-
cies, and hundreds of groups generate genome and transcriptome
assemblies of just single species. Because most journals require
only the raw sequencing data to be submitted to NCBI/ENA/
DDBJ, genome and transcriptome assemblies and annotations are
often stored at university servers or digital repositories.
At diArk, we manually track the availability of genome and
transcriptome assemblies by browsing publications, genome data-
bases of species and taxa from large-scale efforts and small research
communities, and the NCBI genome assembly database [13].
While diArk includes almost all available genome assemblies, man-
ually keeping track with the pace of transcriptome assembly gen-
eration is more difficult. In case of the 1KP and MMETSP projects
hundreds of transcriptome assemblies were made available at once,
and these assemblies have not yet been integrated into diArk. At
diArk, we not only provide links to assembly data but also provide
the genome and transcriptome data directly [14, 15]. For many
species, updated and/or alternative genome assemblies are avail-
able. Alternative genome assemblies have been generated by using
different software on the same sequencing read data, or by inde-
pendent sequencing and assembling efforts. diArk provides meta-
data for each assembly such as date of generation, version,
sequencing method, and assembly software used, and reports sim-
ple statistics such as number of entries (contigs, supercontigs, etc.),
total sequence length, GC content, and N50. This chapter explains
how to use diArk’s search and filter tools, and how genome and
transcriptome data are displayed.
How to Use diArk 3
2 Methods
2.1 diArk Website diArk’s home page offers several entry points to search for
Navigation sequenced genomes and transcriptomes (Fig. 1). The main access
to tools and information is via the dark-grey menu bar near the top
of the page which is present on all diArk pages and facilitates quick
navigation to the search tools, to extensive statistical analyses of the
data, to help pages and other information. In addition to the menu
items, the website provides two autocompletion search forms. An
autocompletion search box, which can be added to the search
plugins of the Firefox browser, is located on the right site of the
menu bar and provides quick access to species summary pages
(Fig. 1A; see Subheading 2.2). Right in the middle of the website
is an autocompletion search field by which a search using the Fast
Search functionalities is started (Fig. 1B; see Subheading 2.3). The
home page also includes a quick view on a randomly selected spe-
cies, a short list of the latest species and their genome/transcriptome
assembly data added to diArk, a short list of the most recent pub-
lications about species’ genome/transcriptome analyses, and a
small box to the right with some metrics of diArk’s content
(Fig. 1C). More statistics can be obtained by clicking the info-icon
in the header of this box, and by browsing the statistics subpage,
which is accessible from the menu bar.
Because many species (especially fungi and yeasts) are known
under multiple, synonymously used scientific names, and because
many species were renamed recently because of better classification
based on now available whole-genome data, we adhered to a few
conventions from the beginning of the diArk project. First, diArk’s
reference scientific species names are the main species entries as
given in the NCBI-Taxonomy database [16]. There is no notifica-
tion by NCBI-Taxonomy, and thus we only adjust names as soon
as we observe changes. Second, as an exception to this convention,
we consistently use the fungi’s teleomorph names as diArk’s scien-
tific reference names. Teleomorph and anamorph are the sexual
and asexual states, respectively, of fungi, and both states were often
given different scientific names in times of pure morphological
classification. Many of these states were later shown to belong to
the same holomorph (the whole fungus, including anamorph and
teleomorph) but all scientific names remained in use. NCBI-
Taxonomy does not have, to our knowledge, a convention on how
to assign a main species name to these fungi. In most cases, the
name of the most widely analysed state seems to be taken.
Accordingly, in case the anamorph is the main experimental
research state for a fungus, the corresponding genome/transcrip-
tome assemblies at diArk refer to the less used teleomorph name.
Third, different sequenced strains/breeds/cultivars/isolates of the
same species (summarized as “strains” from here on) get different
Fig. 1 diArk home page. The dark-grey menu bar below the page header can be used to quickly navigate to
search tools, statistical representations of sequenced genome/transcriptome data, help pages and more. (A)
Use the autocompletion search box to access species summary pages. The menu bar and the search box are
visible from all diArk pages. (B) Entering a search text in the autocompletion search form and selecting a spe-
cies from the list of hits starts the Fast Search. (C) Some metrics on diArk’s content are shown in the right box.
More numbers will be shown upon clicking the info-icon
entries in diArk to facilitate distinguishing multiple genome/

transcriptome assemblies of the same species. Sometimes, this
information cannot be revealed and the respective assemblies are
combined under a common species entry without strain informa-
tion. These assemblies (and also multiple assemblies of identical
strains) are numbered consecutively.
To facilitate the search for sequenced genomes/transcriptomes
in case researchers only know a common name but not the scien-
tific name (or one of the multiple used scientific names) the species
How to Use diArk 5
are tagged by “alternative” and synonymously used scientific names

and by common names, which are all fully available for the key-
word search.
2.2 The Fastest Species summary pages provide the most basic information about
Access to Sequenced available genome and transcriptome assembly data. These pages
Genome are accessed by using the autocompletion search box in the menu
and Transcriptome bar which is present on all diArk pages (Fig. 1A). The query is
Data automatically performed in all species name categories, diArk’s
main scientific names, alternative/synonymous scientific names,
names of anamorphs, and common names. The search box can be
added to the list of search plugins of the Firefox browser by click-
ing on the Firefox browser icon on the right site of the search box.
This allows accessing diArk’s species summary pages from
anywhere.
1. To access a species summary page, first open the diArk home
page (http://www.diark.org) (Fig. 1). Locate the autocomple-
tion search box in the right top corner of the page.
2. To find a sequenced eukaryote of interest, start typing your
query into the search box (e.g., type “dict”). The autocomple-
tion function will list the first 10 hits for your query string in
alphabetical order and summarize the remaining if more hits
were found. Direct matches of the query string to diArk’s main
species names are shown in bold. In case the query string
matched to a common name, a name of an anamorph or an
alternative scientific name, diArk’s main species name is shown
in the list (e.g., type “dolphin,” “chicken,” or “duck”).
3. Move the mouse to the name of your eukaryote of interest. For
faster orientation, the currently activated species name is high-
lighted in yellow. Click on the name of the eukaryote of interest
to open the species summary page (e.g., click on “Dictyostelium
discoideum AX4”).
4. On top of the species summary page is a header with diArk’s
main species name in bold and a brief taxonomic overview with
the three most ancient and the three most recent taxa (Fig. 2A).
The page lists species-related information such as full taxonomy,
alternative and common species names, comments about spe-
cific strains sequenced, and provides links to NCBI taxonomy
and Encyclopedia of Life pages (Fig. 2B). The project-related
part of the page lists the type of data (genomic DNA or tran-
scribed DNA) and the sequencing centers where the data have
been obtained from (Fig. 2C). Via the links you can directly go
to the sequencing centers’ reference pages for the respective
species. The projects also list and provide links to community-
driven species home pages such as dictyBase, XenBase, or
ZFIN. Using these links you can directly access more
Fig. 2 Species summary page. (A) Header with species name and basic taxonomy. (B) Complete species infor-
mation including full taxonomy and alternative scientific, common and anamorph names. (C) List of all external
resources that provide access to genome/transcriptome assembly data for the particular species.
How to Use diArk 7
species-related data and analysis tools. If the genome and/or

transcriptiome assemblies of the species have already been pub-
lished, these data are listed in the Publications section.
5. The lower part of the species summary page contains the
Genome files section which is sorted by projects (Fig. 2D). For
each project the sequence data available is tabulated. The table
provides a quick overview about assembly version, assembly
release date, genome assembly completeness, sequencing cover-
age (if known), GC content, assembly size, contig number,
presence of illegal characters in the data (not being g/G, a/A,
t/T, c/C, or n/N), and the N50 of the dataset. These data
allow an easy comparison if multiple versions of the same data,
different assembly states (e.g., contigs vs. supercontigs vs. chro-
mosome; Table 1), and alternative assemblies (indicated by “_
assembly”) are available. In addition, the Genome files tables
contain icons that can be clicked for more detailed information.
Click on the info-icon in the contigs column to view N50 (con-
tigs sorted by lengths) and A50 (cumulated assembly length by
contig number) plots (Fig. 3A). Clicking the Chaos Game
Representation (CGR) fingerprint icon provides the CGR of
the assembly and Frequency Chaos Game Representations
(FCGRs) of the data in all resolutions up to 1024 × 1024
(Fig. 3B). Click the arrow-down button in the Acc column to
see accession numbers, if available. The chromosome icon in
the File column allows access to the assembly data in archived
fasta format. Click the Seq info icon to get further information
about the sequencing method (e.g., Sanger, Roche/454,
Illumina, and PacBio) and the assembly software. The back-
ground color of the Seq info icon indicates the sequencing
method with, for example, blue being used for Sanger, red for
Roche/454, and yellow for Illumina sequencing.
6. In case multiple strains have been sequenced for the same spe-
cies, only one can be selected from the search box list. The
Genome files sections are collapsed if multiple species are
shown, but can be opened by clicking Show genomes. If you
want to get a quick overview about all sequenced strains, use
the Taxonomy Search Module (see Subheading 2.4).
2.3 The Fast Search The Fast Search is enabled by using the autocompletion search
field in the middle of the home page or by selecting Search Database
from the menu bar. The autocompletion function in the search
Fig. 2 (continued) Some of these external resources provide extensive additional data and multiple analyses
tools. (D) List of assembly files available at diArk sorted by project. In case several projects host exactly the
same data, these data are linked. The table contains multiple metrics for comparing different assemblies and
evaluating the quality of each assembly. Multiple icons provide further detailed information and plots upon
clicking
Table 1
Genome and transcriptome assembly file types
Chromosome Every fasta-entry in this file is a chromosome. There are a

few exceptions where chromosomes are split in two or
more fasta-entries.
Uchromosome These files contain contigs/supercontigs which could not
be mapped to any (unknown chr.) or anchored (random
chr.) to a certain chromosome.
Supercontigs Every fasta-entry represents a supercontig which consists of
sorted contigs separated by estimated or fixed numbers of
“N” bases.
Usupercontigs These files contain contigs which could not be mapped to
supercontigs.
Ultracontigs Every fasta-entry represents a number of supercontigs
assembled to an ultracontig.
Contigs Contigs (from “contiguous sequence”) are the smallest
pieces of an assembly and consist of overlapping sequence
reads.
Ureads These files contain the unplaced reads, reads that could not
be assembled to contigs. These files are especially
important for low-coverage genomes that in most cases
end up with very short contigs. In these cases, small
proteins or some exons can be reconstructed from the
ureads-files.
Apicoplast These files contain the apicoplast DNA. The apicoplast is a
relict, nonphotosynthetic plastid found in Apicomplexa.
It is proposed that it evolved via secondary
endosymbiosis. The apicoplast is surrounded by four
membranes within the outermost part of the
endomembrane system.
Chloroplast These files contain the chloroplast DNA. Chloroplasts are
organelles found in plant cells and eukaryotic algae that
conduct photosynthesis.
Kinetoplast These files contain the kinetoplast DNA. A Kinetoplast is a
disk-shaped mass of circular DNAs inside a large
mitochondrion that contains many copies of the
mitochondrial genome. Kinetoplasts are only found in
protozoa of the class kinetoplastea. Kinetoplasts are
usually adjacent to the organisms’ flagellar basal body
leading to the thought that they are tightly bound to the
cytoskeleton.
Plastid These files contain plastid DNA. Plastids are major double-
membrane organelles found in the cells of plants, algae,
and some other eukaryotic organisms.
(continued)
How to Use diArk 9
Table 1
(continued)
Mito These files contain the mitochondrial DNA. Mitochondria

are membrane-enclosed organelles found in most
eukaryotic cells.
Nucleomorph These files contain nucleomorph DNA. Nucleomorphs are
small, vestigial eukaryotic nuclei found between the inner
and outer pairs of membranes in certain plastids. So far,
nucleomorphs have only been identified in
cryptomonads, which belong to the Chromista
supergroup, and in chlorarachniophytes, which are a
subphylum of Rhizaria.
TSA Transcriptome shotgun assembly.
_assembly This extension is used to distinguish multiple assemblies of
the same strain/breed/cultivar/isolate. Different
assemblies can be based on using the same sequencing
data but different assembly software and protocols, or are
the result of sequencing and assembling the same strain/
breed/cultivar/isolate multiple times.
_haploid This extension to an assembly type indicates that the data
(e.g., contigs, supercontigs) have been merged to
generate an assembly representing a haploid state.
_diploid This extension to an assembly type indicates that both
alleles were assembled independently.
Fig. 3 Genome assembly analyses. (A) By clicking the info-icon in the Contigs column of the Genome files sec-
tion of the species summary page, the user can inspect N50 and A50 plots of the assemblies. (B) A Chaos
Game Representation (CGR) is a unique fingerprint for each genome dataset and the number of pixels in the
graph is exactly the number of nucleotides in the dataset. Therefore, for comparing CGRs usually Frequency
Chaos Game Representations (FCGRs) are taken, in which the pixels in a certain resolution-dependent section
of the graph are summed
field works similar to that in the autocompletion search box in the

menu bar (see Subheading 2.2). However, small pictures of the
species, if available, allow easier identification of the species of
interest, and additional information is provided for each species in
terms of linked project pages and available genome assembly files.
In contrast to the species summary pages, the Fast Search allows
easy extension or filtering of the search space by selecting/dese-
lecting species, and the Results tabs provide full information about
species and assembly file related data.
1. Go to diArk’s home page and enter “dict” in the autocomple-
tion search field in the middle of the page.
2. Use the up- and down-keys and press enter, or use the mouse
to select “Dictyostelium discoideum AX4 | Dd” and start the
Fast Search.
3. The Fast Search contains a headline summarizing filter param-
eters (Fig. 4), which were preselected and combined from the
extended Search Modules from the complex search (see
Subheading 2.4). Below the headline are short sections separating
filter for species names, several taxa and model organisms, and a
few options to filter by sequencing type, completeness of
sequencing, and availability of genome assembly files for down-
load in diArk (Fig. 4A). The small exclamation mark icons next
to model organism names indicate, that genome/transcriptome
assemblies are available for multiple strains/breeds/cultivars/
isolates and that only the most commonly used is selected (e.g.,
in the case of Caenorhabditis elegans the Bristol N2 strains, and
for Saccharomyces cerevisiae the S288c strain). The Sequencing
type filter allows selecting those species for which only EST,
genome or RNAseq data or for which multiple data types are
available.
4. Move further down the page to inspect the Search Results
which are organized in multiple tabs (Fig. 4B). By default the
Species result view is opened summarizing species related
information, links to species sequencing centers and other
resources with assembly data, and publications. This result tab
is organized species by species. The Projects result view is
organized by sequencing center allowing a resource-centric
view on the data in case multiple species were selected. The
Publications result view summarizes all publications related to
the selected species. The Genome Stats result view provides a
Fig. 4 (continued) Below the species selection section there are three options to select certain sequencing
types (genome, EST, transcriptome, and combinations of these), complete or incomplete genomes, and genome
data available for download at diArk. (B) Data for the selected species can be browsed in seven Result tabs.
By default, the Species result tab is opened which is identical to the species section on the species summary
page (see Fig. 2B). Here, the References result tab is opened providing information about available analysis
tools and data types at species home pages and repositories
How to Use diArk 11
Fig. 4 The Fast Search. (A) The Fast Search offers a collection of the most commonly used search options.
Species can be searched using an autocompletion search field and are selected by pressing the enter key
or the left mouse button. Species and taxa can also be selected from the list of model organisms and taxa.
quick overview about chromosome numbers (if known),

genome assembly size, GC content, and contig numbers. This
view is especially useful for comparing multiple strains or closely
related species. By default, the analysis data for the suspected
most complete assembly (size of the largest available assembly)
are shown. The Genome Files result view provides the same
information as the Genome files section of the species summary
pages (Fig. 2D). The References result view provides further
information about the availability of genome map viewers
(GBrowse or JBrowse) and BLAST servers (TBLASTN and
BLASTP, which also indicates availability of protein annota-
tions), and the possibility to obtain cDNA clones for further
research (Fig. 4C). The Sequencing Stats result view provides
multiple plots, which are obviously only available and useful if
multiple species were selected.
5. Move up the page again and reset the Fast Search by clicking on
“Fast search” in the menu bar. Select “Mammalia” from the
taxa. Automatically, “Primates” and “Rodentia” are also
selected, as well as human and mouse from the Model
Organisms. Dashes in the selection fields from “Metazoa” and
“Chordata” indicate selection of a subset of the respective taxa.
At the bottom of the Search section, the number of selected
species and related publications/projects are given. Select/
deselect “Primates” and/or “Rodentia” to see the interplay
between the various selection fields and the influence on the
filtered results. In the default Species result view, the selected
species are sorted by “Taxonomy.” The order can be changed
to sorting by “Name” and the number of visible species
adjusted. Browse through the other Result tabs to see how the
information is organized in case multiple species are selected.
Go to the Genome Stats tab to compare the genome assembly
sizes (Fig. 5).
6. Move up again to the Search for species input field, enter
“danio” and select the “Brachydanio rerio str. Tuebingen” for
comparison.
2.4 Complex In the extended search, available by Search Database and then
Searches Search from the menu bar, the database is searched using modules
by Combining Search that can be combined in any order. These modules work as selec-
Modules tion baskets, meaning that by default nothing is selected when
choosing a search module. Users are usually interested in only a
small subset of the data, and this is faster to select from the avail-
able options than to deselect the rest. There are five different mod-
ules each providing specific options: a module for the full-text
search in all species names, a taxonomy search module, a publica-
tion search module, a module to search sequencing project related
data, and a module to filter by parameters related to
genome/transcriptome assembly files. A search operation can con-
sist of any combination of modules and their options. By adding
Fig. 5 The Genome Stats result view. The Genome Stats result view shows the genome size and GC content for
the selected species, here all mammals. To better evaluate these metrics the number of contigs for the under-
lying dataset is given. In most cases the sizes of the contig datasets are bigger than those of supercontigs and
chromosomes because the latter do not contain those contigs that cannot be ordered into supercontigs or
mapped to chromosomes
further search modules the user can successively refine the search
and narrow down the result list. For each module the resulting set
of species, projects and publications is shown below the modules,
providing additional context. When a new module is added the
options available are restricted by the selection from the previous
module(s). At any time, the search options for every module can
be changed and modifications are propagated down the chain
reapplying previous user actions.
1. Click on Search Database and then Search in the menu bar
to move to the extended search by Search Modules (Fig. 6).
By default, all data in the database are selected and can be
browsed using the Search Result tabs as described above (see
Subheading 2.3).
2. The Species Names search module is identical to the species
autocompletion search field available in the Fast Search
(Fig. 4A). Click on the Taxonomy search module picture. The
headline contains a search module icon and the search module
name on the left, and a number of icons on the right (Fig. 7A).
Fig. 6 Search modules for the extended search. The extended search allows any combination of the available
five search modules to select specific subsets of the species and to filter for certain assembly characteristics.
When opening the search from the menu bar, all species are selected by default. By selecting any search
module all previous data (either all or the selection from previous search modules) are blocked. By selecting
species/publications/projects from the search modules these data immediately become available in the Result
views
Fig. 7 (continued) contracting the module (arrow-up/arrow-down icon). (B) Section of the Taxonomy search
module that allows selecting any combination of species from a full taxonomic tree. Here, “Dictyostelium
discoideum AX4” was searched and selected in the autocompletion field, which opened the corresponding part
of the tree up to the searched species. Species connected to internal nodes are automatically shown. The tree
can be expanded and contracted using the arrow-down/arrow-up icons, and species and taxa are selected
using the check boxes
Fig. 7 The Taxonomy search module. (A) The header of the Taxonomy search module. The icons in the right top
corner of the header are available in all search modules and allow removing the module (minus icon), getting
explanations for the search options (help icon), activating/deactivating the module (check box), and expanding/
Another random document with
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colleagues, assumed the chief command. The French and
Austrians reoccupied the French Legation, but the barricade in
Customs-street was lost. One German only was killed and the
position was saved, but the blunder might have been
disastrous.
"It was obvious from the first that the great danger at the
British Legation was not so much from rifle-fire as from
incendiarism, for on three sides the compound was surrounded
by Chinese buildings of a highly inflammable nature. Before
time could be given to clear an open space round the Legation,
the buildings to the rear of Mr. Cockburn's house were set on
fire, and as the wind was blowing strongly towards us it
seemed as if nothing could prevent the fire from bursting into
the Legation. Water had to be used sparingly, for the wells
were lower than they had been for years, yet the flames had to
be fought. Bullets were whistling through the trees. Private
Scadding, the first Englishman to fall, was killed while on
watch on the stables near by. Men and women lined up, and
water passed along in buckets to a small fire engine that was
played upon the fire. Walls were broken through, trees hastily
cut down, and desperate work saved the building. It was the
first experience of intense excitement. Then the men set to
with a will, and till late at night were demolishing the
temple and buildings outside the wall of the Legation. Work
was continued in the morning, but when it was proposed to pull
down an unimportant building in 'the Hanlin Academy that abuts
upon the Legation to the North, the proposition was vetoed.
Such desecration, it was said, would wound the
susceptibilities of the Chinese Government. It was 'the most
sacred building in China.' To lay hands upon it, even to
safeguard the lives of beleaguered women and children, could
not be thought of, for fear of wounding the susceptibilities
of the Chinese Government! So little do the oldest of us
understand the Chinese.
"A strong wind was blowing from the Hanlin into the Legation,
the distance separating the nearest building from the
Minister's residence being only a few feet. Fire the one and
the Minister's residence would have been in danger. Suddenly
there was the alarm of fire. Smoke was rising from the Hanlin.
The most venerated pile in Peking, the great Imperial Academy,
centre of all Chinese learning, with its priceless collection of
books and manuscripts, was in flames. Everyone who was off
duty rushed to the back of the Legation. The Hanlin had been
occupied during the night by Imperial soldiers, who did not
hesitate, in their rage to destroy the foreigners, to set fire
to the buildings. It was first necessary to clear the temple.
A breach was made in the wall, Captain Poole headed a force of
Marines and volunteers who rushed in, divided, searched the
courts, and returned to the main pavilion with its superb
pillars and memorial tablets. Chinese were rushing from other
burning pavilions to the main entrance. They were taken by
surprise and many were killed, but they had done their evil
deed. … To save the Legation it was necessary to continue the
destruction and dismantle the library buildings. With great
difficulty, with inadequate tools, the buildings were pulled
down. Trees endangering our position were felled. An attempt
was made to rescue specimens of the more valuable manuscripts,
but few were saved for the danger was pressing. Sir Claude
MacDonald, as soon as the fire was discovered, despatched a
messenger to the Tsung-li-Yamên, telling them of the fire and
urging them to send some responsible officials to carry away
what volumes could be rescued, but no attention was given to
his courteous communication. The Dutch Legation was burned on
the 22nd, and next day Chinese soldiers set fire to the
Russo-Chinese Bank, and a greater part of the buildings were
destroyed, involving in danger the American Legation. Chinese
volunteers were called for. They responded readily, worked
with much courage exposed to fire from the wall, and the
Legation was saved. All the buildings back from the bank to
the Chien Mên (the main gate between the Chinese and Tartar
cities facing the entrance to the Forbidden City) seemed to be
on fire. Then all the Customs buildings were fired, so that
flames were on every side, and the smoke was tremendous, while
the fusillade was incessant. An Italian and a German died of
their wounds. The first American was killed, shot from the
wall, then a Russian fell. They were dropping off one by one,
and already we were well accustomed to the sight of the
stretcher and the funeral. Wounded were being brought in from
every Legation to the hospital in the British Legation. …
{121}
"Then a new terror was added to the fears of the besieged, for
the Imperial troops mounted a 3 in. Krupp gun on the Chien Mên,
the gate opposite to the Forbidden City, and began throwing
segment shells from a distance of 1,000 yards into the crowded
Legation. The first shell struck the American Legation, others
burst over the British compound, while others crashed into the
upper rooms of the German Legation. It was known that the
Chinese had ten similar guns in Peking, while we had nothing
with which to answer their fire, and no one ever knew where
the next gun might be mounted. Immediately all hands dug
bomb-proof shelters for the women and children. Rifle fire
also played on the Americans from the wall quite close to them
at a distance of a few hundred feet only, whence, safely
sheltered by the parapet of the wall, men could enfilade the
barricade which was held by the Americans on the street
running east and west under the wall. The barricade became
untenable, and to occupy the wall was a paramount necessity
which could no longer be delayed. … Down in the besieged area
the enemy pressed upon every side. Again they attempted to
fire the British Legation from the Mongol market on the west;
but a sortie was made by British Marines and Volunteers, and
the Chinese were driven from house to house out of the market.
The work was dangerous, and Captain Halliday was dangerously
wounded, while Captain Strouts had an extraordinary escape,
the bullet grazing the skin above the carotid artery. The
sortie was entirely successful; some rifles were captured, and
ammunition, which was more precious than silver. The buildings
were then fired by us, the fire being kept under control,
which cleared a long distance round the west of the Legation.
Fortification proceeded without intermission and all the
defences of the besieged area quickly gathered strength. For
the first time in war, art was a feature in the fortification.
Sandbags were of every colour under the sun and of every texture.
Silks and satins, curtains and carpets and embroideries were
ruthlessly cut up into sandbags. In the Prince's Fu the
sandbags were made of the richest silks and satins, the
Imperial gifts and accumulated treasures of one of the eight
princely families of China. In the Prince's Fu the Chinese
made a determined attempt to force their way into the Palace
in their frenzy to slaughter the native Christians. In the
angle of the wall in the northeastern court of the Palace they
made a breach in the wall and rushed wildly in. But the
Japanese were waiting for them and from loopholes they had
made opposite rolled them over like rabbits, driving them
helter-skelter back again. Some 20 were killed, and but for
the unsteadiness of the Italians who were assisting the
Japanese the execution would have been greater. The Chinese
were driven back, but the same evening they threw fireballs of
petroleum over the wall and set fire to the building. Flames
spread to the splendid main pavilion of the Palace. The
Japanese in their turn were driven back, and the Christians
escaping from the burning building overflowed from the Fu into
all that quarter lying between the Palace grounds and
Legation-street.
"On June 25 a truly Oriental method of weakening our defence

was attempted by the Chinese. Up to 4 o'clock in the afternoon
the shooting of rifles and field guns had been continuous,
when suddenly bugles were sounded north, east, south, and
west, and, as if by magic, the firing ceased. It was under
perfect control—Imperial control commanded by responsible
central authority. The silence abruptly following the
fusillade was striking. Then an official of low rank was seen
to affix to the parapet of the north bridge near the British
Legation a board inscribed with 18 Chinese
characters:—'Imperial command to protect Ministers and stop
firing. A despatch will be handed at the Imperial Canal
Bridge.' A placard whereon was written 'Despatch will be
received' was sent by one of the Chinese clerks employed in
the Legation, but when he approached the bridge a hundred
rifles from the Imperial Palace gate were levelled at him. The
despatch was never received. The artifice deceived no one.
Treachery was feared, vigilance was redoubled. Sandbags were
thrown on positions which during fire were untenable. So that
when at midnight the general attack was made upon us we were
prepared, and every man was at his post. The surprise had
failed. As firing had ceased so it began. Horns were sounded,
and then from every quarter a hail of bullets poured over us,
sweeping through the trees and striking with sharp impact the
roofs of the pavilions. No harm was done though the noise was
terrific. Great steadiness was shown by the men. They lay
quietly behind the sandbags and not a shot was fired in reply.
It was suggested as an explanation of this wild firing that
the shots were to kill the guardian spirits which were known
to hover over us. Similar fusillades took place at the
American Legation and at the French Legation, and with the
same result. During the armistice the Chinese had availed
themselves of the quiet to throw up earthworks in the Carriage
Park alongside the British Legation, in the Mongol market
between the British and Russian Legations, and at both ends of
Legation-street facing the Americans on the west and facing
the French Legation corner on the east.
"Our isolation was now complete, and the enemy's cordon was
constantly drawing closer. Every wall beyond the lines was
loopholed. Not only was the besieged area cut off from all
communication with the world outside Peking, but it was cut
off from all communication with the Pei-tang. No messenger
could be induced for love or money to carry a message there.
Bishop Favier and his guards must have been already hard
pressed, for they were exposed to the danger not only of rifle
and cannon, but of fire and starvation. The small garrison
detached from the guards was known to be inadequately supplied
with ammunition. It was known, however, that the danger of the
situation had long been foreseen by Monseigneur Favier, who,
speaking with unequalled authority, had weeks before the siege
vainly urged his Minister to bring troops to Peking. When the
crisis became inevitable and Christian refugees poured into
the city the Bishop endeavoured to buy arms and ammunition, so
that there was a hope, though a faint one, that the Chinese
themselves had assisted in the defence. So with stores. Large
quantities of grain were stored in the Pei-tang, but whether
sufficient for a siege for a garrison of 3,000 souls was not
known. Their condition was a constant source of anxiety to the
Europeans within the Legations, who were powerless to help
them. Watch was kept unceasingly for any sign of the disaster
that seemed inevitable—the massacre and the conflagration.
{122}
"Towards evening of the 28th a Krupp gun was mounted in the

Mongol market, not 300 yards from the British Legation, and
fire was opened upon a storeyed building occupied by marines
in the south court of the Legation. Fired at short range, the
shells crashed through the roof and walls. For an hour the
bombardment continued, but no one was injured, though a crack
racing pony in the stables below was killed, and next day
eaten. It was determined to capture this gun, so in the early
morning a force consisting of 26 British, ten Germans, ten
Russians, five French, and five Italians, and about 20
volunteers made a sortie from the Legation to try and capture
the gun and burn the houses covering it; but the attempt was a
fiasco. The men got tangled up in the lanes so that the reserve
line with the kerosene marched ahead of the firing line; there
was a Babel of voices, no one knew where to go, the captain
lost his head and set fire to the houses in the rear and the
men retreated pell-mell. … The Chinese, however, were alarmed
and removed the gun. Meanwhile both French and German
Legations had suffered heavily. …
"On the 29th the French Legation was hard pressed. One of
their officers, the midshipman Herbert, was shot.
Reinforcements were hastily sent from the Fu, and the attack
was repulsed; but some of the outer buildings of the Legation
were burned, and the French had to retire further into the
Legation. In this siege it was striking what a powerful part
petroleum was made to play. Already the French Legation had
suffered more severely than any other Legation; of their 45
men 16 had been killed or wounded. Krupp guns had been mounted
not 50 yards to the eastward, and the eastern walls of the
pavilions were being gradually and systematically battered
into ruins. All day now and until the cessation of hostilities
shells were pounding into the French Legation, into Chamot's
hotel, and from the Chien Mên on the wall, promiscuously,
everywhere. Much property was destroyed, but, though the
shells burst everywhere and escapes were marvellous, few
people were hit. Bullets whistled in the Legation compounds.
Surgeon Lippett was talking to Mr. Conger in the American
Legation when he was hit by a bullet that smashed the thigh
bone. Had the bullet not struck the surgeon it would have hit
the Minister. Mr. Pethick was sitting at a window of the
American Legation fanning himself when a bullet pierced the
fan. A civilian was wounded in the British Legation, and a
marine, Phillips, was killed while walking in the compound.
A fragment of shell fell on a patient inside the hospital.
"The cordon was drawing closer. In the Fu nearly one-third of

the buildings had been abandoned and the Japanese retired to a
second line of defence. Shells were fired by the hundred. On
the 29th 70 shells were thrown into the British Legation. The
difficulty of holding the American and German barricades on
the city wall was increasing. The positions were very much
exposed. A Krupp gun was brought close to the American
barricade. The Russo-Chinese Bank and all the buildings near
were occupied by Chinese troops, the walls being loopholed and
lanes barricaded. And all were so close that you could not
look through a loop-hole without being shot at. Yet the
American barricade, with its mixed guard of Americans,
Russians, and British, had to be held at all hazards;
otherwise the Krupp gun could be brought down the wall and
play havoc upon the Legations, the furthest of which—the
British—was at its nearest point not 400 yards distant. Still
more exposed than the American barricade was the outpost on
the wall held by the Germans. At first they had been
reinforced by the French and Austrians, but the needs of the
French Legation were equally pressing and the guards were
withdrawn and a small picket of British sent to aid the
Germans. … In the morning of July 1 the Chinese climbed up the
ramp and surprised the guard. The order was hastily given to
retire, and the picket, shaken by its losses of yesterday,
left the wall. The German non-commissioned officer who gave
the order was severely blamed for thus abandoning a position
that he had been ordered to hold. Withdrawal left the
Americans exposed in the rear. They saw the Germans retire,
and in a panic fell back to the Legation, rushing pell-mell
down the ramp. Nothing had occurred at the barricade itself to
justify the retreat, although two men had fallen within a few
hours before. Yet the wall was the key of the position and had
to be maintained. A conference was held at the British
Legation, and as a result orders were given to return to the
post. Captain Myers at once took back a strong detachment of
14 Americans, ten British, and ten Russians, and reoccupied
the barricade as if nothing had happened. The Chinese,
ignorant that the post had been evacuated, lost their
opportunity. Then the guard in the French Legation was driven
a stage further back and M. Wagner, a volunteer, was killed by
the bursting of a shell. …
"It was a day of misfortunes. In the afternoon the most

disastrous sortie of the siege was attempted. A Krupp gun,
firing at short range into the Fu (i. e., the Prince's
Palace), was a serious menace to our communications. Captain
Paolini, the Italian officer, conceived the idea that he could
capture the gun if volunteers could be given him and if the
Japanese could assist. … By this ineffective sortie our small
garrison was reduced by three men killed, one officer and four
men and one volunteer wounded. Fortunately it was no worse.
The gun that was not captured was brought up again next day
into play and continued battering down the Fu walls. The enemy
were working their way ever nearer to the refugee Christians.
Their rage to reach the Christians was appalling. They cursed
them from over the wall, hurled stones at them, and threw
shells to explode overhead. Only after the armistice, when we
received the 'Peking Gazette,' did we find that word to burn
out and slaughter the converts had come from the highest in
the land. The Japanese were driven still further back. Already
they had lost heavily, for upon them had fallen the brunt of a
defence the gallantry of which surpassed all praise. When the
siege was raised it was found that of the entire force of
marines only five men had escaped without wounds; one was
wounded five times. Colonel Shiba early raised a force of
'Christian volunteers,' drilled them, instructed them, and
armed them with rifles captured from the enemy. They made an
effective addition to the Japanese strength. …
{123}
"At daybreak on July 3, the Chinese barricade on the top of

the wall near the American outpost was successfully stormed by
a party of British, Americans, and Russians, under the leadership
of Captain Myers, Captain Vroublevsky, and Mr. Nigel Oliphant.
… The position was intolerable. It was imperative to rush the
barricade and drive out the Chinese; nothing else could be
done. An attack was planned for 3 in the morning, and before
that hour a strong force of British was sent over from the
legation. The combined force assembled for the attack
consisted of 26 British marines under Sergeant Murphy and
Corporal Gregory, with Mr. Nigel Oliphant as volunteer, 15
Russians under Captain Vroublevsky, and 15 Americans, all
being under the command of Captain Myers. When asked if they
came willingly one American begged to be relieved and was sent
below. This left the total force at 56, of whom 14 were
Americans. So close were the Chinese that it was only a couple
of jumps from our barricade to their fort. There was a rush to
be first over, the fort was stormed, and dashing round the
covering wall the 'foreign devils' charged behind the
barricade. Taken by surprise the Chinese fired in the air,
fled incontinently, and were shot down as they ran along the
open surface of the wall. Captain Vroublevsky and his
detachment acted with especial gallantry, for their duty it
was to attack the Chinese barricade in the front, while the
British and Americans took it in the rear. Two banners marked
'General Ma' were captured. Fifteen Chinese soldiers of
Tung-fuh-siang were killed outright and many more must have
been wounded. Some rifles and ammunition were captured. Then
the allied forces, exposed to a heavy fire, retired within
what had been the Chinese barricade and employed it against
the enemy who had built it. Captain Myers was wounded in the
knee by tripping over a fallen spear, two Americans, Turner
and Thomas—one having accidentally jumped on the wrong side of
the barricade—were killed, and Corporal Gregory was wounded in
the foot. News of the successful sortie gave much pleasure to
the community. Chinese coolies were sent on the wall, and a
strongly intrenched redoubt was built there; the camp was made
safe by traverses. Unfortunately, the wound of Captain Myers
proved more serious than was at first suspected, and he was
not again able to return to duty. The services of a brave and
capable officer were lost to the garrison; his post on the
wall was taken most ably by Captain Percy Smith and other
officers in turn.
"Most of the shelling was now directed against the French and
German Legations and Chamot's Hotel. The hotel was struck 91
times and was several times set on fire, but the flame was
extinguished. Work continued there, however hot the shelling,
for food had to be prepared there for half the community in
Peking, Russians, French, Germans, and Austrians. The energy
of Chamot was marvellous. He fed the troops and a crowd of
Christian refugees, killed his own mules and horses, ground
his own wheat, and baked 300 loaves a day. Shelled out of the
kitchen he baked in the parlour. His courage inspired the
Chinese, and they followed him under fire with an amazing
confidence.
"Then suddenly a new attempt was made to reduce the British

Legation. Guns firing round shot, eight-pounders and
four-pounders, were mounted on the Imperial City wall
overlooking from the north the Hanlin and the British
Legation. With glasses—the distance was only 350 yards—one
could clearly see the officers and distinguish their Imperial
Peacock feathers and Mandarin hats. … Three batteries in all,
carrying five guns, were mounted on the Imperial City wall
where the bombardment could be witnessed by the Empress
Dowager and her counsellors, and day after day round shot were
thrown from them into the British Legation, into a compound
crowded with women and children. … On July 5 Mr. David
Oliphant, of the British Legation, was killed. He was felling
a tree by the well in the Hanlin when he was shot by a sniper
concealed in a roof in the Imperial Carriage Park, and died
within an hour. Only 24 years of age, he was a student of
exceptional promise and ability. …
"Day by day the Chinese were pressing us more closely. In the

Fu they were gradually wedging their way in from the
north-east so as to cut the communications between the British
and the Legations to the east. They burned their way from house
to house. Keeping under cover, they set alight the gables
within reach by torches of cloth soaked in kerosene held at
the end of long poles. If the roof were beyond reach they
threw over fireballs of kerosene, or, if still further, shot
into them with arrows freighted with burning cloth. In this
way and with the use of the heavy gun they battered a way
through the houses and courtyards of the Prince's Palace. A
daring attempt made by the Japanese to capture the gun
resulted in failure. Coolies failed them when they were within
four yards of success, and they were forced to retire. Their
gallant leader Captain Ando was shot in the throat while
waving on his men, one marine was seriously wounded, and one
Christian volunteer killed. … By the 8th the position in the
Fu was alarming, for the Japanese force had been reduced to 13
marines and 14 volunteers; yet with decreasing numbers they
were constantly called upon to defend a longer line.
Reinforcements were sent them of half-a-dozen Customs and
student volunteers and of six British marines. Nothing can
give a better indication of the smallness of our garrison than
the fact that throughout the siege reinforcements meant five men
or ten men. Strong reinforcements meant 15 men. Our
reinforcements were counted by ones, not by companies. With
this force a line of intrenchments stretching from the outer
court of the Fu on the east across the grounds to near the
extreme northwest corner was held till the end. … The position
was one of constant solicitude, for the loss of the Fu would
have imperilled the British Legation. A Krupp gun, mounted 50
yards away, had the range and raked the post with shell and
shrapnel. To strengthen the breastwork exposure to rifle fire
was incurred from 20 yards' distance, while to reach the post
required crossing a zone of fire which was perhaps the hottest
in the whole of the defences. Many men were wounded there, and
one Italian had his head blown off. Shell fire finally made it
impossible to live there. The advanced posts were abandoned,
and the sentries fell back to the main picket. No sooner was
the advanced post abandoned than it was occupied by the
Chinese, and the defences we had made were turned against us.
{124}
"Meanwhile, the French and German Legations were being roughly

handled, and men were falling daily. At the German Legation
shells burst through the Minister's drawing-room. Most of the
other buildings conspicuous by their height were
uninhabitable, but every member of the Legation remained at
his post. So, too, in the French Legation, where the Austrians
were, Dr. and Madame von Rosthorn remained by the side of
their men. The French volunteers and Dr. Matignon stood
stanchly by their Legation, although it was fast tumbling into
ruins, their coolness and resolution being in curious contrast
to the despair of their Minister, who, crying, 'Tout est perdu,'
melodramatically burned the French archives in a ditch at the
British Legation. Chinese and French were so close that the
voices of the Chinese officers could be heard encouraging
their men. Chinese were within the Legation itself. Their guns
literally bombarded the Minister's residence 'à bout portant,'
and the noise of the exploding shells was terrific. Yet the men
never flinched. … July 11 was a day of many casualties. One
German was mortally wounded; one Englishman, one Italian, and
one Japanese were seriously wounded. Mr. Nigel Oliphant, a
volunteer, received a bullet wound in the leg, while Mr.
Narahara, the well-known secretary of the Japanese Legation,
wounded by the bursting of a shell, suffered a compound
fracture of the leg, which from the first gave cause for
anxiety. He gradually sank and died on July 24. …
On the 11th 18 prisoners were captured by the French in a

temple near the Legation. They were soldiers, and a Chinese
Christian gave information as to their whereabouts. Everyone
of them was put to death without mercy in the French Legation,
bayoneted by a French corporal to save cartridges. Questioned
before death they gave much information that was obviously
false. One man, however, declared that a mine was being driven
under the French Legation. His story had quick corroboration.
As the afternoon of the 13th was closing a feint attack was
made on the Japanese intrenchments in the Fu. Then the sound
of many bugles was heard from the camps round the French
Legation, to be followed in a few minutes by a terrific
explosion, and in a moment or two by another; and bricks and
debris were hurled into the air. It was a dull roar in the
midst of the devilish cries of hordes of Chinese, shrieking
like spirits in hell, the rattle of musketry, and the boom of
heavy guns. The mine of which the prisoner had warned us had
exploded and burst an entrance into the French Legation. When
the first mine exploded the French Captain Darcy, the Austrian
Charge d'Affaires, two French marines, and Mr. Destelan of the
Customs were standing over the death-trap. Mr. Destelan was
buried up to the neck, but was rescued unhurt, the two marines
were engulfed and their bodies were never recovered, Captain
Darcy and Dr. von Rosthorn escaped miraculously. The latter
was buried by the first explosion and released unhurt a moment
or two later by the second. Driven out of the main buildings,
the small garrison (it consisted only of 17 Austrians with
three officers, 27 French with two officers, and nine
volunteers) fell back a few paces to a line of defence, part
of which had only been completed in the afternoon, and
securely held the position.
"Simultaneously with this attack upon the French Legation the

Chinese made a determined assault upon the German Legation,
the effective strength of whose garrison numbered only one
officer and 31 men. They broke into the Club alongside the
Legation and were on the tennis ground when Count Soden and a
handful of German soldiers gallantly charged them at the point
of the bayonet and drove them out headlong. … Uniforms on the
dead Chinese showed that the attack had been carried out by
the troops of Yung Lu, reinforced by the savages of
Tung-fuh-siang. Some of the dead were armed with the latest
pattern Mauser and the newest German army revolver. Some
ammunition, of which the guards were in much need, was
recovered and distributed among the Japanese and Italians.
Firing continued round the other Legations; every battery
opened fire; the air hissed with bullets. There was momentary
darkness, then flames broke out from the large foreign houses
between the German Legation and Canal-street. It seemed at one
time as if the whole of the quarter would be burned, but the
fire did not spread. Heavy rain came on, and the rest of the
night passed in quiet.
"On July 14, a messenger, sent out on the 10th, with a letter
for the troops, returned to the British Legation. He had been
arrested by the Chinese, cruelly beaten, and taken, he said,
to the yamên of Yung Lu, and there given the following letter,
purporting to be written by Prince Ching 'and others,'
addressed to the British Minister. It was the first
communication of any kind whatsoever that had reached us from
outside for nearly one month. 'For the last ten days the
soldiers and Militia have been fighting, and there has been no
communication between us, to our great anxiety. Some time ago
we hung up a board, expressing our intentions, but no answer
has been received, and contrary to expectation the foreign
soldiers made renewed attacks, causing alarm and suspicion
among soldiers and people. Yesterday the troops captured a
convert named Chin Ssu-hei and learnt from him that all the
foreign Ministers 'were well, which caused us very great
satisfaction. But it is the unexpected which happens. The
reinforcements of foreign troops were long ago stopped and
turned back by the "Boxers," and if, in accordance with
previous agreement, we were to guard your Excellencies out of
the city, there are so many "Boxers" on the road to Tien-tsin
and Ta-ku that we should be apprehensive of misadventure. We
now request your Excellencies to first take your families and
the various members of your staffs, and leave your Legations
in detachments. We should select trustworthy officers to give
close and strict protection, and you should temporarily reside
in the Tsung-li-Yamên, pending future arrangements for your
return home, in order to preserve friendly relations intact
from beginning to end. But at the time of leaving the
Legations there must on no account whatever be taken any
single armed soldier, in order to prevent doubt and fear on
the part of the troops and people, leading to untoward
incidents. If your Excellencies are willing to show this
confidence, we beg you to communicate with all the foreign
Ministers in Peking, to-morrow at noon being the limit of
time, and to let the original messenger deliver the reply in
order that we may settle the day for leaving the Legations.
This is the single way of preserving relations which we have
been able to devise in the face of innumerable difficulties.
If no reply is received by the time fixed, even our affection
will not enable us to help you.
Compliments.
(Signed) Prince Ching and others.
July 14, 1900.'
{125}
"Following as it did immediately after the attack on the

French Legation, which reduced it to ruins, the letter did not
lack for impudence. 'Boxers' had driven back our troops,
'Militia,' not 'Boxers,' had been attacking us in Peking. The
letter was read with derision. It was interpreted as a
guileless attempt to seduce the Ministers away from their
Legations and massacre them at ease. News we heard
subsequently had just reached the Chinese of the taking of
Tien-tsin city. … On the 15th a reply was sent declining on
the part of the foreign representatives the invitation to
proceed to the Tsung-li-Yamên, and pointing out that no
attacks had been made by our troops, who were only defending
the lives and property of foreigners against the attacks of
Chinese Government troops. The reply concluded with a
statement that if the Chinese Government wished to negotiate
they should send a responsible official with a white flag. …
"The morning of the 16th opened with a disaster. Captain

Strouts, the senior British officer, was shot while returning
from the outposts in the Fu. He was struck in the upper part
of the left thigh by an expanding bullet, and died an hour
after being brought into the hospital, to the grief of the
entire community. … While shells were bursting in the trees,
and amid the crack of rifle bullets, the brave young fellow to
whose gallant defence we all owed so much was laid to rest. …
While the service was proceeding a messenger bearing a flag of
truce was approaching the gate. … The letter was from 'Prince
Ching and others.' It explained that the reason for suggesting
the removal of the Legations to the Tsung-li-Yamên was that
the Chinese Government could afford more efficient protection
to the members of the Legations if concentrated than if
scattered as at present. As the foreign Ministers did not
agree, however, the Chinese would as in duty bound do their
utmost to protect the Legations where they were. (While the
latter sentence was being read the translator had to raise his
voice in order that it should be heard above the crack of the
Imperial rifle bullets.) They would bring reinforcements and
continue their endeavours to prevent the 'Boxers' from firing,
and they trusted that the foreign Ministers on their part
would restrain their troops also from firing.
"By the same messenger a cipher message was brought to Mr.

Conger, the American Minister. It said:—'Communicate tidings
bearer.' It was in the State Department cipher and had no date
or indication by whom it had been sent. Mr. Conger replied in the
same cipher:—'For one month we have been besieged in British
Legation under continued shot and shell from Chinese troops.
Quick relief only can prevent general massacre.' When
forwarding his reply he asked that it should be sent to the
address from which the other had come, which address had not
been communicated to him. Next day the Yamên sent him an
answer saying that his message had been forwarded and
explaining that the telegram sent to him had been contained in
a telegram from Wu Ting Fang, the Chinese Minister at
Washington, dated July 11. This telegram read:—'The United
States cheerfully aid China, but it is thinking of Mr.
Minister Conger. The Hon. Secretary of State inquires after
him by telegram, which I beg to be transmitted to him and get
his reply.' From this we could well imagine what specious
assurances had been given to Mr. Hay by Wu Ting Fang's bland
assurances that there had been a most regrettable outbreak on
the part of lawless bands in the north of China which the
Government was vainly struggling to cope with. … From July 17
there was a cessation of hostilities; not that men were not
wounded afterwards and Christian coolies fired upon whenever
they showed themselves, but the organized attacks ceased and
the Krupp guns were muzzled. Fearing treachery, however, we
relaxed none of our vigilance. Trenches were cut where mines
might have been driven. All walls and shelters were so
strengthened as to be practically shell-proof. Our
preparations were purely defensive. On their part the Chinese
also continued work at their barricades. From their barricade
on the top of the wall near the German Legation they advanced
westward so that they could fire directly down into the German
Legation and pick off men going up the steps of the Minister's
house. They built a wall with loop-holes across
Legation-street not 20 yards from the Russian barricade. In
nearly every position the enemy were so close that you could
shoot into the muzzles of their rifles thrust through the
loop-holes. The cordon was still drawn tightly round us, and
we were penned in to prevent our acting in co-operation with
the troops who were coming to our relief. No provisions were
permitted to reach us, but a few eggs for the women and
children were surreptitiously sold us by Chinese soldiers. All
were on reduced rations, the allowance for the 2,750 native
Christians whom we had to provide for being barely sufficient
to save them from starvation. Their sufferings were very
great, the mortality among the children and the aged pitiful.
No one could have foreseen that within the restricted limits
of the besieged area, with the food supply therein obtainable,
473 civilians (of these 414—namely, 191 men, 147 women, 76
children—were inside the British Legation), a garrison of 400
men, 2,750 refugees, and some 400 native servants could have
sustained a siege of two entire months. Providentially in the
very centre of Legation-street there was a mill with a large
quantity of grain which turned out 900 lb. of flour a day
divided between the hotel and the Legation. One day the
Tsung-li-Yamên insultingly sent us a present of 1,000 lb. of
flour and some ice and vegetables, but no one would venture to
eat the flour, fearing that it might be poisoned.
Communications now passed almost daily with the Tsung-li-Yamên
or with the officials whose despatches were signed 'Prince
Ching and others.' On July 17, Sir Claude MacDonald replied to
the suggestion that the Ministers would restrain their troops
from firing upon the Chinese. He said that from the first the
foreign troops had acted entirely in self-defence, and would
continue to do so. But the Chinese must understand that
previous events had led to a want of confidence and that if
barricades were erected or troops moved in the vicinity of the
Legations the foreign guards would be obliged to fire. In the
afternoon the Chinese replied, reviewing the situation and
ascribing the hostilities to the attacks previously made by
the Legation guards. They noted with satisfaction that a
cessation of firing was agreed to on both sides, but suggested
that as foreign soldiers had been firing from the city wall
east of the Chien Mên, they should be removed from that
position.
{126}
Next day, Sir Claude MacDonald replied with a review of the
situation from the foreign point of view. … He hoped that
mutual confidence would gradually be restored, but meanwhile
he again pointed out that cessation of hostile preparations as
well as firing was necessary on the part of the Chinese troops
to secure that the foreign troops should cease firing. As for
the suggestion that the foreign troops should leave the city
wall, it was impossible to accede to it, because a great part
of the attacks on the Legations had been made from the wall.
He concluded by suggesting that sellers of fruit and ice
should be allowed to come in. They were never permitted to
come in. It was clear, however, that events were happening
elsewhere to cause alarm in the Imperial Court. On the
afternoon of the first day of what might be called the
armistice M Pelliot, a French gentleman from Tongking, entered
the Chinese lines and to the great anxiety of all was absent five
hours. He was taken by soldiers to a yamên of one of the big
generals—he knew not which—was plied with questions which,
speaking some Chinese, he could answer, and was sent back
unmolested with an escort of 15 soldiers 'to protect him
against the Boxers.' This unusual clemency was interpreted
favourably. It was clear that the Chinese had sustained a
severe defeat and that relief was coming. Next day direct
communication was for the first time held with an official of
the Tsung-li-Yamên. A secretary named Wen Jui came to the
Legation to see Sir Claude MacDonald and was received by the
Minister outside the gate, not being permitted to enter. He
said that the regrettable occurrences were due to 'local
banditti,' that the Government had great concern to protect
the foreigners, that Baron von Ketteler's body had been
recovered from the hands of the 'local banditti' who had
murdered him and been enclosed in a valuable coffin. He urged
that the maintenance of foreign troops on the city was
unnecessary and that they should be withdrawn. It was pointed
out to him that, as we had been very continuously shelled from
the city wall both from the Ha-ta Mên and the Chien Mên, it
would be inadvisable to retire. Asked to send copies of the
'Peking Gazette,' he hesitated a moment and then stammered
that he really had not himself seen the 'Peking Gazette' for a
long time, but he would inquire and see if they could be
bought. He never came back and never sent a 'Gazette.' His
name was Wen Jui. When we did obtain copies of the 'Gazette'
it was interesting to find two items that must have been
especially unpleasant for him to have us know. On June 24, by
Imperial decree, leaders were appointed to the 'Boxers,' or
'patriotic militia.' Among the chiefs was Wen Jui.
"The visit of Wen Jui was on the 18th. Up to the time of his
visit, though more than four weeks had passed since the
assassination, no allusion of any kind whatever had been made
in any 'Peking Gazette' to the murder of Baron van Ketteler.
Then the Empress-Dowager, yielding to her fears, published an
allusion to the murder. Will the German Emperor rest satisfied
with the tardy official reference to the brutal assassination
of his Minister by an Imperial officer? 'Last month the
Chancellor of the Japanese Legation was killed. This was,

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Eukaryotic Genomic Databases Martin

Plant Genomic and Cytogenetic Databases Methods in

Secondary Findings in Genomic Research 1st Edition

The Eukaryotic RNA Exosome: Methods and Protocols John

Genomic Medicine: A Practical Guide Laura J. Tafe

Databases Theory and Applications Junhu Wang

Translational Cardiometabolic Genomic Medicine 1st

Seven Databases in Seven Weeks A Guide to Modern

A Code for Carolyn A Genomic Thriller V. Anne Smith

Martin Kollmar Editor

For further volumes:

ISSN 1064-3745 ISSN 1940-6029 (electronic)

Library of Congress Control Number: 2018935916

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Printed on acid-free paper

Göttingen, Germany Martin Kollmar

1 Identifying Sequenced Eukaryotic Genomes and Transcriptomes

12 EchinoBase: Tools for Echinoderm Genome Analyses ��������������������������������������� 349

Julie Agapite · Biological Laboratories, Harvard University, Cambridge, MA, USA

Madeline Crosby · Biological Laboratories, Harvard University, Cambridge, MA, USA

Makedonka Mitreva · McDonnell Genome Institute, Washington University in St. Louis,

David R. Shaw · Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor,

Ying Wang · Xenbase Development Team, Department of Computer Science, University of

Identifying Sequenced Eukaryotic Genomes

Key words Eukaryotes, Sequenced genomes, Genome assembly, Transcriptome assembly

The diArk Eukaryotic Genome Database (http://www.diark.org)

orders of magnitude. Current large scale projects cover all major

entries in diArk to facilitate distinguishing multiple genome/

are tagged by “alternative” and synonymously used scientific names

s­pecies-­related data and analysis tools. If the genome and/or

Chromosome Every fasta-entry in this file is a chromosome. There are a

Mito These files contain the mitochondrial DNA. Mitochondria

field works similar to that in the autocompletion search box in the

quick overview about chromosome numbers (if known),

"On June 25 a truly Oriental method of weakening our defence

"Towards evening of the 28th a Krupp gun was mounted in the

"The cordon was drawing closer. In the Fu nearly one-third of

"It was a day of misfortunes. In the afternoon the most

"At daybreak on July 3, the Chinese barricade on the top of

"Then suddenly a new attempt was made to reduce the British

"Day by day the Chinese were pressing us more closely. In the

"Meanwhile, the French and German Legations were being roughly

On the 11th 18 prisoners were captured by the French in a

"Simultaneously with this attack upon the French Legation the

"Following as it did immediately after the attack on the

"The morning of the 16th opened with a disaster. Captain

"By the same messenger a cipher message was brought to Mr.

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12 EchinoBase: Tools for Echinoderm Genome Analyses �� 349

species-related data and analysis tools. If the genome and/or