Bioinformatics (2001) David Mount
Can be purchased directly from Cold Spring Harbor Press for $75.
This book is one of the few texts on Bioinformatics that give adequate descriptions of the workings of the tools used in the field.

Fundemental Concepts of Bioinformatics (2003) Dan Krane and Michael Raymer
Can be purchased directly from Benjamin Cummings for $66.
Generally more accessible than Bioinformatics.

Begining Perl (2000) Simon Cozens
Can be purchased used from Amazon for $16.00.

Begining Perl for Bioinformatics (2001) James Tisdell
Can be purchased directly from O'Reilly for $39.95.
Pitched to the biologist with no programming experience. A good, readable book when read cover-to-cover, but pretty useless as a reference.