Gene sequence data is the most abundant type of data available, and if you're interested in analyzing it, you'll find a wealth of computational methods and tools to help you. In fact, finding the data is not the challenge at all; rather it is dealing with the plethora of flat file formats used to process the sequence entries and trying to remember what their specific field codes mean. If you survive by surrounding yourself with well-thumbed hard copies of readme files or remembering exactly where to look for the details when you need them, then Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases is for you. This book is a handy resource, as well as an invaluable reference, for anyone who needs to know about the practical aspects and mechanics of sequence analysis. Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis. The book is partitioned into three fundamental areas to help you maximize your use of the content. The first section, "Databases" contains examples of flatfiles from key databases (GenBank, EMBL, SWISS-PROT), the definitions of the codes or fields used in each database, and the sequence feature types/terms and qualifiers for the nucleotide and protein databases. The second section, "Tools" provides the command line syntax for popular applications such as ReadSeq, MEME/MAST, BLAST, ClustalW, and the EMBOSS suite of analytical tools. The third section, "Appendixes" concentrates on information essential to understanding the individual components that make up a biological sequence. The tables in this section include nucleotide and protein codes, genetic codes, as well as other relevant information. Written in O'Reilly's enormously popular, straightforward "Nutshell" format, this book draws together essential information for bioinformaticians in industry and academia, as well as for students. If sequence analysis is part of your daily life, you'll want this easy-to-use book on your desk.

Amazon.com® Reader Reviews (Ranked by Helpfulness)

Average Amazon.com® Rating:  Based on 3 Ratings

from a bioinformatics student and programmer - 2003-04-09
Reviewer Rating:
I picked this book up at BioCon 2003 and, to be honest, I wasn't sure at first how useful it was going to be. Flipping through a few of the sections, it seemed to be little more than an assemblage of man pages for each of the tools and programs it covered. So I put it on a shelf above my monitor at work for a while and as the days went by I found myself grabbing it more and more often to look something up.

For example, I found myself needing reminding of the option for tabular output when doing a psi-blast. Grab the book ... a ha! ... -m 8. You can use the man pages or tutorials for many of things like this but sometimes there is a lot to wade through to find what you were looking for. Also, if you're like me you like the feel of a book sometimes and the ability to scrawl notes in the margins. It's just nice having all the options right there on the page.

To be fair to the authors, I don't think that Chia-hsiu Tu was very accurate in his review by saying that "this books focus on EMBOSS only" (sic). EMBOSS coverage does make up about 58% of the book, but it is a suite of 150 useful programs. Unless you want only a sentence or two about each one you're going to have to use up a few pages. You get just enough info to learn about each and a quick guide to their usage. If you want to know more, there are links to their full documentation online.

Some sections are stronger than others. The MEME/MAST chapter, for instance, doesn't just list out options but has great command line examples and a paragraph for each explaining what is going on. On the other hand, I wanted to use stretcher (in the EMBOSS package) and there was only a quick example (the syntax of which didn't work for me) and a listing of six options. I needed to find out how to make it work in a non-interactive way and write its output to STDOUT, neither of which were illustrated (-auto and -stdout, by the way).

Ok, let's get to what this book covers. The first section goes really in depth to cover the data-exchange formats that we nerds find ourselves writing parsing scripts for all the time. (yes, yes, bioperl, biojava, etc. are great, but they aren't in this book. Hopefully one will cover them soon.) What I found most useful were the example files for each format (EMBL, DDBJ, Genbank, FASTA, SWISS-PROT, PFAM, & PROSITE) and the tables that were laid out for them. For example, there are nice little tables listing every feature (62 at my count) and feature qualifier (74!) that you can expect to find in a DDBJ/EMBL/Genbank file. And for each of those there is a little descripton of what they represent. Very nice.

The second part of the book covers these specific tools: ReadSeq, the BLAST suite (7 progs), BLAT, CLUSTALW, HMMER (10 progs), MEME, MAST, and the EMBOSS suite (~150 progs). These sections are pretty decent and while you won't find much info on how the algorithms behind the programs work, you will have everything you need to run the programs and fine-tune their options to control their behavior.

Lastly, the third part of the book has a really valuable quick reference of a variety of things such as a listing of the amino acids, their 1 and 3-letter abbreviations, structures and properties. In the genetic codes section you'll be able to quickly remind yourself that the transcriptional product for AUA in invertebrate mitochondriates differs from the norm, coding for methionine instead of isoleucine. (you knew that right?)

On the whole, I think this reference is a great review of the most common tools out there for sequence analysis and a quick guide to their use. While at times examples and verbose explanations are lacking, one must keep in mind that this is a book in the "nutshell" series, not in the "definitive guide" one. If you find yourself scouring for online docs and searching man pages for special options often, you should definitely get this book.

Sequence Analysis: Not in a Nutshell - 2003-07-03
Reviewer Rating:
The O'Reilly Press is normally the gold standard when it comes to very well-written and very well-edited hard science documents. That is why I purchased this one. Sadly, this falls very far below the norm. The first 73 pages of the text may be skipped. Most of the rest is EMBOSS. Sadly, you can get this directly, and freely, from the original authors. Just use a normal search and type "EMBOSS". Nothing else pertains.

Wayne

an excellent rteference book - 2003-03-17
Reviewer Rating:
This books focus on EMBOSS only, a high quality open source bioinformatic toolkit. It can be a useful reference book when write web interface of those programs in this book. Also it provides the urls where we can download from? where the original idea come from?