Bioinformatics FAQ (Frequently Asked Questions) - Books

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(Continued from previous part...)

Computational/Mathematical aspects

If you are a hardcore maths/computing person Michael Waterman's "Introduction to Computational Biology" [Chapman & Hall/CRC Statistics and Mathematics; ISBN 0412993910] and Pavel Pevzner's "Computational Molecular Biology - An Algorithmic Approach" [The MIT Press (A Bradford Book); ISBN 0262161974] will give you all the discrete maths you can shake a stick at, but perfunctory introductions to the biology.

Bioinformatics.Org's very own Jeff Bizzaro recommends Dan Gusfield's "Algorithms on Strings, Trees and Sequences" [Cambridge, 1997 ISBN 0-52158-519-8], Richard Durbin, S. Eddy, A. Krogh, G. Mitchison "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" [Cambridge, 1997 ISBN 0-52162-971-3] (which I think is one of the clearest and most comprehensive guides to alignment algorithms) and---for that full "computers-to-biology conversion"--- Geoffrey M. Cooper "The Cell: A Molecular Approach" [ASM Press, 1996 ISBN 0-87893-119-8]. Jeff Ames writes that a second edition of this book is now available [Sinauer Associates, Incorporated, 2000 ISBN 0-87893-106-6] and that this version---if you can find it in the shops---comes with a CD.

Applying bioinformatics to biological research

One outstanding general text for the biologist is David W. Mount's "Bioinformatics" [Cold Spring Harbor Press; ISBN 0879696087]. It's not cheap, but it's the best I've seen if you are studying bioinformatics itself.

Bioinformatics has been dismissed by some as "the science of BLAST searches". The best collection of advice so far on doing BLAST searches is O'Reilly's BLAST book by Ian Korf, Mark Yandell and Joseph Bedell [O'Reilly ISBN 0-596-00299-8]. I reviewed it enthusiastically, but not uncritically, for the UK UNIX Users' Group magazine. I'd go as far as to say that all biologists thinking of using BLAST in their research should read the relevant sections before they even go near a computer.

If you wish to use general bioinformatics tools, especially if you are a little wary of computers, my new "best" book is "Bioinformatics for Dummies" [John Wiley and Sons ISBN 0764516965]. It is (obviously) aimed at people who are beginners, who are happier using the Web rather than typing commands, and who are more interested in learning than in impressing people---the writing is friendly clear and unpretentious. However, like several of my other tips (below) it concentrates on Web-based resources so it will, inevitably, date. (This is partially compensated for by there being a companion Website.)

Also, if you're coming to the subject as a computer user with a biological background, looking to exploit the many tools available, you might want to try Terry Attwood and David Parry-Smith's "Introduction to Bioinformatics" [Longman Higher Education; ISBN 0582327881], or Des Higgins and Willie Taylor's "Bioinformatics: Sequence Structure and Databanks" [Oxford University Press; ISBN 0199637903]. Another excellent practical introduction is Andreas Baxevanis and Francis Oulette's "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins" [Wiley-Interscience; ISBN 0471383910], now in its new and improved second edition. Bax teaches bioinformatics all over Canada and the experience shows. Arthur Lesk has also produced an excellent teaching book particularly for protein bioinformatics in his Introduction to Bioinformatics

Bioinformatics.Org also recommends Cynthia Gibas and Per Jambeck's "Developing Bioinformatics Skills" [O'Reilly, 2001 ISBN 1-56592-664-1].

Stuart Brown recommends his own book "Bioinformatics: A Biologist's Guide to Biocomputing and the Internet" [Eaton Pub Co; ISBN: 188129918X]. If he sends me a review copy I might recommend it too ;-) .

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