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English Pages 296 [297] Year 2021
Virus Bioinformatics
Chapman & Hall/CRC Computational Biology Series About the Series:
This series aims to capture new developments in computational biology, as well as high-quality work summarizing or contributing to more established topics. Publishing a broad range of reference works, textbooks, and handbooks, the series is designed to appeal to students, researchers, and professionals in all areas of computational biology, including genomics, proteomics, and cancer computational biology, as well as interdisciplinary researchers involved in associated fields, such as bioinformatics and systems biology. PUBLISHED TITLES Clustering in Bioinformatics and Drug Discovery John David MacCuish and Norah E. MacCuish Metabolomics: Practical Guide to Design and Analysis Ron Wehrens and Reza Salek An Introduction to Systems Biology: Design Principles of Biological Circuits Second Edition
Uri Alon
Computational Biology: A Statistical Mechanics Perspective Second Edition
Ralf Blossey
Stochastic Modelling for Systems Biology Third Edition
Darren J. Wilkinson Computational Genomics with R Altuna Akalin, Bora Uyar, Vedran Franke, and Jonathan Ronen An Introduction to Computational Systems Biology: Systems-level Modelling of Cellular Networks Karthik Raman
Virus Bioinformatics Dmitrij Frishman and Manja Marz
For more information about this series please visit: https://www.routledge.com/Chapman--HallCRC-ComputationalBiology-Series/book-series/CRCCBS
Virus Bioinformatics
Edited by
Dmitrij Frishman Manja Marz
First edition published 2022 by CRC Press 6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742 and by CRC Press 2 Park Square, Milton Park, Abingdon, Oxon, OX14 4RN © 2022 Dmitrij Frishman & Manja Marz CRC Press is an imprint of Taylor & Francis Group, LLC Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all m aterial reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any i nformation storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, access www. copyright.com or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 9 78-750-8400. For works that are not available on CCC please contact [email protected] Trademark Notice: Product or corporate names may be trademarks or registered trademarks and are used only for identification and explanation without intent to infringe. Library of Congress Cataloging‑in‑Publication Data Names: Frishman, Dmitrij, editor. | Marz, Manuela, editor. Title: Virus bioinformatics / edited by Dmitrij Frishman, Manuela Marz. Description: First edition. | Boca Raton : CRC Press, 2021. | Series: Chapman & Hall/CRC computational biology series | Includes bibliographical references and index. Identifiers: LCCN 2021008505 | ISBN 9780367558604 (hardback) | ISBN 9780367564193 (paperback) | ISBN 9781003097679 (ebook) Subjects: LCSH: Virology—Data processing. | Virology—Research. | Bioinformatics. Classification: LCC QR370.V57 2021 | DDC 579.0285—dc23 LC record available at https://lccn.loc.gov/2021008505 ISBN: 978-0 -367-55860-4 (hbk) ISBN: 978-0 -367-56419-3 (pbk) ISBN: 978-1-003-09767-9 (ebk) Typeset in Minion Pro by codeMantra
Contents Preface, vii Editors, xi Contributors, xiii CHAPTER 1
◾
Comparative Genomics of Viruses
1
THOMAS R ATTEI
CHAPTER 2
◾
Current Techniques and Approaches for Metagenomic Exploration of Phage Diversity
17
SIMON ROUX AND MARK BORODOVSKY
CHAPTER 3
◾
Direct RNA Sequencing for Complete Viral Genomes
35
SEBASTIAN KRAUTWURST, RONALD DIJKMAN, VOLKER THIEL, ANDI KRUMBHOLZ, AND MANJA MARZ
CHAPTER 4
◾
Computational Methods for Viral Quasispecies Assembly
51
KIM PHILIPP JABLONSKI AND NIKO BEERENWINKEL
CHAPTER 5
◾
Functional RNA Structures in the 3′ UTR of Mosquito-Borne Flaviviruses
65
MICHAEL T. WOLFINGER, ROMAN OCHSENREITER, AND IVO L. HOFACKER
v
vi ◾ Contents
Chapter 6 ◾ Structural Bioinformatics of Influenza Virus RNA Genomes
101
Alexander P. Gultyaev, René C.L. Olsthoorn, Monique I. Spronken, and Mathilde Richard
Chapter 7 ◾ Structural Genomics and Interactomics of SARS-COV2: Decoding Basic Building Blocks of the Coronavirus
121
Ziyang Gao, Senbao Lu, Oleksandr Narykov, Suhas Srinivasan, and Dmitry Korkin
Chapter 8 ◾ Computational Tools for Discovery of CD8 T cell Epitopes and CTL Immune Escape in Viruses Causing Persistent Infections
141
Hadi K arimzadeh, Daniel Habermann, Daniel Hoffmann, and Michael Roggendorf
Chapter 9 ◾ Virus-Host Transcriptomics
157
Caroline C. Friedel
Chapter 10 ◾ Sequence Classification with Machine Learning at the Example of Viral Host Prediction 179 Florian Mock and Manja Marz
Chapter 11 ◾ Master Regulators of Host Response to SARS-CoV-2 as Promising Targets for Drug Repurposing 197 Manasa K alya, K amilya Altynbekova, and Alexander Kel
Chapter 12 ◾ The Potential of Computational Genomics in the Design of Oncolytic Viruses 245 Henni Zommer and Tamir Tuller
Chapter 13 ◾ Sharing Knowledge in Virology Edouard De Castro, Chantal Hulo, Patrick Masson, and Philippe Le Mercier
INDEX, 275
263
Preface
T
his book was conceived long before the start of the COVID-19 pandemic. While there are multiple excellent publications covering various aspects of bioinformatics—from sequence analysis and structural bioinformatics to regulation and genome evolution—we felt that a dedicated book on bioinformatics of viruses would be warranted given their remarkable and very special properties, which render many standard algorithms and methods inefficient and dictate the application of highly specialized tools. As this book progressed toward completion, the actual scale of the COVID-19 pandemic became apparent, giving further emphasis to the importance of the field. Indeed, at least half of the chapters in this book mention the SARS-COV-2 virus, and two chapters are dedicated to it. We have described only a tiny fraction of the estimated total number of viruses (