Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins
By addebook • Jul 2nd, 2009 • Category: Biology
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins
by: Andreas D. Baxevanis, B. F. Francis Ouellette
en
0471191965 9780471191964 9780585240879
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins
By Andreas D. Baxevanis, B. F. Francis Ouellette
Publisher: Wiley-Interscience
Number Of Pages: 384
Publication Date: 1998-07-14
ISBN-10 / ASIN: 0471191965
ISBN-13 / EAN: 9780471191964
Binding: Paperback
BIOINFORMATICS, a field integrating molecular biology and computational methods, has revolutionized gene discovery and related research. This new, rapidly evolving discipline provides the tools scientists need to cope with the flood of biological data and raw DNA and protein sequence information generated by such endeavors as the Human Genome Project.
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins makes computational biology accessible to scientists at all levels of expertise, including those with no formal computer training. It cuts through the overwhelming array of existing tools and databases, helping the reader design and implement a successful sequence analysis strategy. Presented by leading authorities in computational biology, this edited volume covers the gamut of topics, from using software and Internet resources to submitting DNA sequences to databases. Other topics include:
* The GenBank sequence database and structure databases
* Sequence analysis using GCG
* Information retrieval from biological databases
* The NCBI data model
* Sequence alignment and database searching
* Practical aspects of multiple sequence alignment
* Phylogenetic analysis
* Predictive methods using nucleotide sequences and protein sequences
* Navigating public physical mapping databases
* ACeDB: A database for genome information
Bioinformatics is fully referenced and provides appendices, sample sequence file formats, and over 120 illustrations. A must have for molecular biologists, geneticists, and any biologist interested in genes and proteins, it can also be used in a one-semester practical course on sequence analysis and bioinformatics.
Summary: Not a very useful textbook at all
Rating: 3
I agree with the reviewer who said that this book is poorly organized. Actually, I would summarise this book with a single saying: TMI (Too Much Information)! In teaching you how to accomplish a simple task, the details given are tremendous, so much so that you can’t see the forest from the trees and you end up having to navigate the bioinformatics Web sites by trial and error anyway. Perhaps this book would be useful for a post-doc or someone already very familiar with those sites and want to know how they work. For the student (undergrad through Master), I suggest picking up the short-n-sweet paperback ‘Bioinformatics’ by Westhead, Parish & Twyman instead.
Summary: Bent edges
Rating: 3
Book came quickly but edges were bent, not like a new book. Returned it and got full refund.
Summary: Somewhat more than an out-of-date catalog of tools
Rating: 3
The book is a collection of chapters by different authors addressing software tools for various problems: database search, multiple sequence alignment, gene prediction, protein structure prediction, etc. A big flaw is that all of the authors assume a different level of prior background and have rather different emphases.
I’d have to agree with the other reviewer that Chapters 1 & 17, which constitute 10% of the book, are wasted paper. No one in 2001 (when the book was published), let alone 2004, needs Chapter 1’s lengthy explanation of what e-mail and web browsers are. And the perl program at the anticlimax of Chapter 17 was … anticlimactic.
The book is to a great extent a catalog of available software tools. With the exception of the chapters on multiple alignment and phylogeny, the emphasis is on not on how the tools work but how to operate them — to the of saying "at this URL there is a web page where you can either paste in your sequence or upload a file". The idea of invoking a program through a Unix command line is more than once presented as a truly daunting prospect. The authors generally do a good job of emphasizing that the programs are the beginning of analysis and not the end; the results must always be viewed somewhat skeptically with an expert eye.
If you’re coming at the book as a biologist, you will probably find it to be a useful catalog of software, though undoubtedly dated by now. If you’re coming at it from the informatics side, you’re going to need some background… a book like Dwyer’s, Setubal and Meidanis’s, or Mount’s will get you up to speed on the algorithm aspects of the field with simplified versions of many of the big problems. Then you can look at this book to find good pointers to the ways the real-world versions have been addressed.
The book was published three years ago and, being to a large extent an index of the work of others, is necessarily no longer up to date in a fast-moving field. It needs a revision and, in the meantime, it would make more sense to snag a used copy than to pay full price for a new book.
Summary: A survey for tool users
Rating: 4
Like any survey, it seems to touch the major features only. And, as others have pointed out, the tools change but the book doesn’t.
I think this is a good, brief introduction to the wide variety of bioinformatic tools and databases on the internet. It describes the major features of each, and the kinds of results that each tool is good for. After that, the serious user will go to the sources of each tool or database, to learn more about the specifics as of the moment. No book can hope to keep up with the weekly enhancements at the major repositories.
I emphasize that this is for tools users, not tool makers. It addresses the working scientists who already know their subjects and their needs. This skips over the algorithms in favor of higher level descriptions, and skips over many of the biological reasons for the tools described. Better-informed tool users get better answers from the tools, true. At some point, though, the biologists want to skip the theory, skip the introduction to subjects in which they’re experts, and get on with their science. I don’t think this book was ever meant for people – and I’m one – who want full details of the algorithms.
I agree, the book treats its many subjects in a shallow way. I think that is by intent, since the book’s real goal is breadth and its target is a reader who knows the basic science. It’s a bit off the center of my interests, but I’ve found it helpful.
Summary: Bioinformatic for the beginner…
Rating: 4
I guess that everybody interrested by this kind of book knows already a little about bioinformatic and wants to improve his bioinformatician skill. So forget about this book:
This is really a well-documented introduction to all the methods currently used by every biologist or biology student, such as Blast, Clustal, multiple alignement or use of web-interface for submiting sequence.
So get it if you need a clear introduction to the field, but if you already know a little bit about bioinfo, immediately choose a more detailed book.
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