You may also wish to add:

• Bioinformatics Computing, by Bryan Bergeron
• Developing Bioinformatics Computer Skills, by Cynthia Gibas and Per Jambeck
• BLAST, by Ian Korf, Mark Yandell and Joseph Bedell
• Bioinformatics in the Post-Genomic Era Genome, Transcriptome, Proteome, and Information-Based Medicine, by Jeff Augen

All of which (and possibly more) are available on O'Reilly's Safari.

Update: Oh, and Sequence Analysis in a Nutshell: A Guide to Tools, by Scott Markel and Darryl Leon, which was on Safari but has been taken down. Still available in print, though, AFAIK.

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