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Paul M. Selzer · Richard J. Marhöfer
Oliver Koch
Applied
Bioinformatics
An Introduction
Second Edition
Including
Exercises
and Solutions
Applied Bioinformatics
Paul M. Selzer
Richard J. Marhöfer
Oliver Koch
Applied
Bioinformatics
An Introduction
Second Edition
Paul M. Selzer
Boehringer Ingelheim
Animal Health
Ingelheim am Rhein, Germany
Oliver Koch
TU Dortmund University
Faculty of Chemistry
and Chemical Biology
Dortmund, Germany
Richard J. Marhöfer
MSD Animal Health
Innovation GmbH
Schwabenheim, Germany
The first edition of this textbook was written by Paul M. Selzer,
Richard J. Marhöfer, and Andreas Rohwer
Originally published in German with the title:
Angewandte Bioinformatik 2018
ISBN 978-3-319-68299-0
ISBN 978-3-319-68301-0
https://doi.org/10.1007/978-3-319-68301-0
Library of Congress Control Number: 2018930594
© Springer International Publishing AG, part of Springer Nature 2008, 2018
This work is subject to copyright. All rights are reserved by the Publisher, whether the
whole or part of the material is concerned, specifically the rights of translation, reprint-
ing, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any
other physical way, and transmission or information storage and retrieval, electronic
adaptation, computer software, or by similar or dissimilar methodology now known or
hereafter developed.
The use of general descriptive names, registered names, trademarks, service marks, etc.
in this publication does not imply, even in the absence of a specific statement, that such
names are exempt from the relevant protective laws and regulations and therefore free
for general use.
The publisher, the authors and the editors are safe to assume that the advice and infor-
mation in this book are believed to be true and accurate at the date of publication. Nei-
ther the publisher nor the authors or the editors give a warranty, express or implied, with
respect to the material contained herein or for any errors or omissions that may have
been made. The publisher remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations.
Printed on acid-free paper
This Springer imprint is published by the registered company Springer International
Publishing AG part of Springer Nature
The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland
(eBook)
V
Preface
Though a relatively young discipline, bioinformatics is finding increasing
importance in many life science disciplines, including biology, biochemistry,
medicine, and chemistry. Since its beginnings in the late 1980s, the success of
bioinformatics has been associated with rapid developments in computer sci-
ence, not least in the relevant hardware and software. In addition, biotechno-
logical advances, such as have been witnessed in the fields of genome
sequencing, microarrays, and proteomics, have contributed enormously to the
bioinformatics boom. Finally, the simultaneous breakthrough and success of
the World Wide Web has facilitated the worldwide distribution of and easy
access to bioinformatics tools.
Today, bioinformatics techniques, such as the Basic Local Alignment Search
Tool (BLAST) algorithm, pairwise and multiple sequence comparisons, queries
of biological databases, and phylogenetic analyses, have become familiar tools
to the natural scientist. Many of the software products that were initially unin-
tuitive and cryptic have matured into relatively simple and user-friendly prod-
ucts that are easily accessible over the Internet. One no longer needs to be a
computer scientist to proficiently operate bioinformatics tools with respect to
complex scientific questions. Nevertheless, what remains important is an
understanding of fundamental biological principles, together with a knowledge
of the appropriate bioinformatics tools available and how to access them. Also
and not least important is the confidence to apply these tools correctly in order
to generate meaningful results.
The present, comprehensively revised second English edition of this book is
based on a lecture series of Paul M. Selzer, professor of biochemistry at the
Interfaculty Institute for Biochemistry, Eberhard-Karls-University, Tübingen,
Germany, as well as on multiple international teaching events within the frame-
works of the
EU FP7
and
Horizon 2020
programs. The book is unique in that it
includes both exercises and their solutions, thereby making it suitable for class-
room use. Based on both the huge national success of the first German edition
from 2004 and the subsequently overwhelming international success of the first
English edition from 2008, the authors decided to produce a second German
and English edition in close proximity to each other. Working on the same
team, each of the three authors had many years of accumulated expertise in
research and development within the pharmaceutical industry, specifically in
the area of bioinformatics and cheminformatics, before they moved to different
career opportunities to widen their individual industrial and academic scien-
tific areas of expertise. The aim of this book is both to introduce the daily appli-
cation of a variety of bioinformatics tools and provide an overview of a complex
field. However, the intent is neither to describe nor even derive formulas or
algorithms, but rather to facilitate rapid and structured access to applied bioin-
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