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Bioinformatics with Python
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python在生物信息学科的应用
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Bioinformatics with
Python Cookbook
Third Edition
Use modern Python libraries and applications to solve
real-world computational biology problems
Tiago Antao
BIRMINGHAM—MUMBAI
Bioinformatics with Python Cookbook
Third Edition
Copyright © 2022 Packt Publishing
All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted
in any form or by any means, without the prior written permission of the publisher, except in the case
of brief quotations embedded in critical articles or reviews.
Every eort has been made in the preparation of this book to ensure the accuracy of the information
presented. However, the information contained in this book is sold without warranty, either express
or implied. Neither the author, nor Packt Publishing or its dealers and distributors, will be held liable
for any damages caused or alleged to have been caused directly or indirectly by this book.
Packt Publishing has endeavored to provide trademark information about all of the companies and
products mentioned in this book by the appropriate use of capitals. However, Packt Publishing cannot
guarantee the accuracy of this information.
Publishing Product Manager: Devika Battike
Senior Editor: David Sugarman
Content Development Editor: Joseph Sunil
Technical Editor: Rahul Limbachiya
Copy Editor: Sas Editing
Project Coordinator: Farheen Fathima
Proofreader: Sas Editing
Indexer: Pratik Shirodkar
Production Designer: Shankar Kalbhor
Marketing Coordinator: Priyanka Mhatre
First published: June 2015
Second edition: November 2018
ird edition: September 2022
Production reference: 1090922
Published by Packt Publishing Ltd.
Livery Place
35 Livery Street
Birmingham
B3 2PB, UK.
ISBN 978-1-80323-642-1
www.packt.com
Contributors
About the author
Tiago Antao is a bioinformatician who is currently working in the eld of genomics. A former computer
scientist, Tiago moved into computational biology with an MSc in bioinformatics from the Faculty
of Sciences at the University of Porto, Portugal, and a PhD on the spread of drug-resistant malaria
from the Liverpool School of Tropical Medicine, UK. Post his doctoral, Tiago worked with human
datasets at the University of Cambridge, UK and with mosquito whole-genome sequencing data at the
University of Oxford, UK, before helping to set up the bioinformatics infrastructure at the University
of Montana, USA. He currently works as a data engineer in the biotechnology eld in Boston, MA.
He is one of the co-authors of Biopython, a major bioinformatics package written in Python.
About the reviewers
Urminder Singh is a bioinformatician, computer scientist, and developer of multiple open source
bioinformatics tools. His educational background encompasses physics, computer science, and
computational biology degrees, including a Ph.D. in bioinformatics from Iowa State University, USA.
His diverse research interests include novel gene evolution, precision medicine, sociogenomics, machine
learning in medicine, and developing tools and algorithms for big heterogeneous data. You can visit
him online at urmi-21.github.io.
Tiany Ho works as a bioinformatics associate at Embark Veterinary. She holds a BSc from the
University of California, Davis in genetics and genomics, and an MPS from Cornell University in
plant breeding and genetics.
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