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Genomic Perl: From Bioinformatics Basics to Working Code [Hardcover]

Rex A. Dwyer


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Book Description

16 Dec 2002 052180177X 978-0521801775 Har/Cdr
This introduction to computational molecular biology will help programmers and biologists learn the skills needed to start work in this important, expanding field. The author explains many of the basic computational problems and gives concise, working programs to solve them in the Perl programming language. With minimal prerequisites, the author explains the biological background for each problem, develops a model for the solution, then introduces the Perl concepts needed to implement the solution. The book covers pairwise and multiple sequence alignment, fast database searches for homologous sequences, protein motif identification, genome rearrangement, physical mapping, phylogeny reconstruction, satellite identification, sequence assembly, gene finding, and RNA secondary structure. The concrete examples and step-by-step approach make it easy to grasp the computational and statistical methods, including dynamic programming, branch-and-bound optimization, greedy methods, maximum likelihood methods, substitution matrices, BLAST searching, and Karlin-Altschul statistics. Perl code is provided on the accompanying CD.

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'I came away from this book not just with more knowledge about genetics and biology - indeed, siome of what I learnt has been directly applicable to some work I have - but also with an understanding of some of the complexity of the problems geneticists face. It fully satisfied its goals, expressed in the preface: teaching computer scientists the biological underpinnings of bhioinformatics … for the programmer like me, interested in what biologists do and how we can helpo them do it, it's by far the clearest introduction available, and I would heartily recommend it.' Simon Cozens

'Genomic Perl gives a balanced and hands-on introduction to a set of algorithms and ideas central to the current practice of bioinformatics. its clear writing and no-frills approach to each topic should appeal to students as well as to university teachers, while providing computational biologists with a concise handbook of the 'greatest hits' in their field.' Naturwissenschaften

'… I found this to be an excellent book, and would not hesitate to recommend it to advanced undergraduate and postgraduate students.' Computing Reviews

'I found the descriptions and discussions to be very good, and one can easily follow along and, in fact, easily adapt the algorithms to other programming languages. this is a nice book for those who want to learn about writing programs for solving bionformatic problems, or for those teaching courses on this (or related) subjects.' Journal of the American Statistical Association

Book Description

There are many basic computational problems in molecular biology and this text gives concise, working programs to solve them using Perl. With minimal prerequisites, the author explains the biological background for each problem, develops a model for the solution, then introduces the Perl concepts needed to implement the solution. Perl code is provided on the accompanying CD.

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Amazon.com: 3.7 out of 5 stars  3 reviews
16 of 20 people found the following review helpful
1.0 out of 5 stars Not a good perl programming book period! 17 Dec 2003
By A Customer - Published on Amazon.com
Format:Hardcover
This books tries to combine and explain both bioinformatics and perl programming yet fails miserably at both. Though I have taken a class on learning perl this code is difficult to read and poorly explained. The bioinformatics is useless because the examples are simply stupid. For example instead of using free energy to determine RNA folding the author uses hydrogen bonding which is completely irrelavent or predicting species by using %gc or %at content between two organsims also useless. If you are looking for bioinformatics programming tips this book will not help you.
Variables are introduced that are not explained and the program is written in the most condensed possible way making it difficult to read and leaving you wading through each line. I am thankful I have taken programming perl and bioinformatics or this book would be of zero value. If I could I would give this book a -5 stars. Check it out at a library before you BUY!!!!!!! Even if perl.com reviews the book favorably the biology is at best completely WRONG!!! Buy O'Riely's advanced bioinformatics.
5.0 out of 5 stars Five Stars 2 July 2014
By Anup B. - Published on Amazon.com
Verified Purchase
Good book with codes
6 of 12 people found the following review helpful
5.0 out of 5 stars Develops effective genomic toolkits for UNIX, Windows & Mac 22 Mar 2003
By Amazon Customer - Published on Amazon.com
Format:Hardcover|Verified Purchase
Combines intuitive derivations of most key algorithms, thoughtful use of key references to illustrate solutions of main problems with a detailed example, and develop well documented, carefully programmed,perl toolkit. The 65 routines on the CD in UNIX, Windows, and Mac formats perform most of the essential maipulations of GenBank sequences. I only miss Hidden Markov Model routines.
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