The Brazilian Symposium on Bioinformatics (BSB) 2008 was held at Santo Andr�e(Sao ˜ Paulo), Brazil, August 28-30,2008. BSB 2008 was the third sym- sium in the BSB series, although BSB was preceded by the Brazilian Workshop on Bioinformatics(WOB). This previous event had three consecutiveeditions in 2002 (Gramado, Rio Grande do Sul), 2003 (Maca� e, Rio de Janeiro), and 2004 (Bras� ?lia, Distrito Federal). The change from workshop to symposium re?ects the increasing quality and interest behind this meeting. For BSB 2008, we had 41 submissions: 32 full papers and 9 extended - stracts, submitted to two tracks: the main track on Computational Biology and Bioinformatics, and the track Applications of Agent Technologies and Mult- gent Systems to Computational Biology.The currentproceedings contain 14 full papers and5 extended abstractsthat wereaccepted. Thesepapers andabstracts were carefully refereed and selected by an international Program Committee of 35 members, with the help of 13 additional reviewers. We believe that this v- ume represents a ?ne contribution to current research in computational biology and bioinformatics, as well as in molecular biology.

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This book constitutes the refereed proceedings of the Third Brazilian Symposium on Bioinformatics, BSB 2008, held in Sao Paulo, Brazil, in August 2008 - co-located with IWGD 2008, the International Workshop on Genomic Databases.

The 14 revised full papers and 5 extended abstracts were carefully reviewed and selected from 41 submissions. The papers address a broad range of current topics in computational biology and bioinformatics featuring original research in computer science, mathematics and statistics as well as in molecular biology, biochemistry, genetics, medicine, microbiology and other life sciences.

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