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15 of 17 persons found the following review helpful.
from a bioinformatics student and programmer
By Joshua Orvis
I picked this book up at BioCon 2003 and, to be honest, I wasn't sure at firstborn how utile 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 ofttimes to look something up.
For example, I found myself requiring reminding of the option for tabular output when doing a psi-blast. Grab the book ... a ha! ... -m 8. You may use the man pages or tutorials for some of things like this but from time to time 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 on occasion and the capacity to scrawl notes in the margins. It's just nice having all the choices right there on the page.
To be reasonable to the authors, I don't think that Chia-hsiu Tu was very precise in his review by saying that "this books focus on EMBOSS only" (sic). EMBOSS coverage does make up when it comes to 58% of the book, but it is a suite of 150 utile programs. Unless you want only a sentence or two when it comes to each one you're going to have to use up a few pages. You get just sufficient data to learn with regards to each and a quick guide to their usage. If you want to recognise more, there are links to their full documentation online.
Some sectionalizations are more inviolable than others. The MEME/MAST chapter, for instance, doesn't just list out choices but has outstanding 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 necessitated to find out how to make it work in a non-interactive way and write it is output to STDOUT, neither of which were illustrated (-auto and -stdout, by the way).
Ok, let's get to what this book covers. The original division goes in truth 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 utile 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 each feature (62 at my count) and feature qualifier (74!) that you may suppose 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 subdivisions are beauteous 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 choices to control their behavior.
Lastly, the third share of the book has a actually valuable quick reference of a potpourri 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 capable to quickly remind yourself that the transcriptional product for AUA in invertebrate mitochondriates is different from the norm, coding for methionine rather of isoleucine. (you knew that right?)
On the whole, I think this reference is a great review of the most mutual tools out there for sequence analysis and a quick guide to their use. While at times examples and verbose explanations are lacking, one ought to 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 particular choices often, you will have to unquestionably get this book.
9 of 11 people found the following review helpful.
Sequence Analysis: Not in a Nutshell
By Wayne J. Becktel
The O'Reilly Press is ordinarily the gold frequent 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 underneath the norm. The firstborn 73 pages of the text may be skipped. Most of the rest is EMBOSS. Sadly, you may get this directly, and freely, from the original authors. Just use a normal search and type "EMBOSS". Nothing else pertains.
Wayne
2 of 6 persons found the following review helpful.
an splendid rteference book
By Chia-hsiu Tu
This books focus on EMBOSS only, a high quality open source bioinformatic toolkit. It may be a utile reference book when write web interface of those programs in this book. Also it provides the urls where we may download from? where the initial idea come from?
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