Ian Korf, Mark Yandell, Joseph Bedell



O'Reilly (2003)




Ivan Uemlianin


April 2004



the lack of quality control will be outweighed by the book's usefulness.

BLAST - the Basic Local Alignment Search Tool - is a set of programs for sequence alignment tasks in bioinformatics. The authors have produced a nicely written and thoughtful text. I cannot highly recommend it however, as the quality control is so poor.

The book suffers from very poor quality control: typos, broken cross-references, code or tables that do not tally with their text, inconsistent equation and citation formatting, unfinished glossary and index. It feels like a rough draft.

The book is in six parts. Part 1 introduces BLAST and walks through a search using BLAST's web interface [1]. Parts 5& 6 include reference material: especially useful as the original programs do not have man pages.

Part 2 reviews molecular biology and approximate string matching. This is sketchy given space constraints, but it's not rushed, and it sticks to the point: to improve your understanding and use of BLAST.

Part 3 looks first at how BLAST uses the theory in part 2, and then puts this in context by discussing usage. This latter discussion is at a higher level to the similar discussion in the reference chapters.

Part 4 discusses installation, and some of the sysadmin necessary when running large analyses on large databases.

A recurrent theme is that BLAST searches should be treated as scientific experiments, and over half of part 3 takes this perspective. The BLAST programs have a vast array of command-line parameters and chapters 8 ('20 tips to improve your BLAST searches') and 9 ('BLAST protocols') discuss how to vary these parameters for common bioinformatic searches or experimental problems.

The discussion on system administration is equally high-level and intelligent, covering such things as local vs remote databases, optimising your hardware, and juggling your available CPU time.

The authors keep a tight rein on the subject matter, and some topics are cut off rather abruptly, especially in part 2, but this is not entirely inappropriate and references are given for further reading.

Notwithstanding its problems, this book is nicely written and well thought out. The writers have done a good job of cementing a fairly concrete collection of themes into a satisfying package.

I can recommend this book for practising bioinformaticians, and sysadmins of commercial or academic establishments. For these people the lack of quality control will be outweighed by the book's usefulness.


Book cover image courtesy of Open Library.

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