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This volume contains the papers selected for presentation at the 4th Brazilian Sym- sium on Bioinformatics, BSB 2009, which was held in Porto Alegre, Brazil, during August 29–31, 2009. The BSB symposium had its origins in the Brazilian Workshop on Bioinformatics (WOB). WOB had three editions, in 2002 (Gramado, RS), in 2003 (Macaé, RJ), and in 2004 (Brasília, DF). The change in the designation from wo- shop to symposium reflects the increase in the quality of the contributions and also in the interest of the scientific community for the meeting. The previous editions of BSB took place in São Leopoldo, RS, in 2005, in Angra dos Reis, RJ, in 2007, and in Santo André, SP, in 2008. As evidence of the internationalization of the event, BSB 2009 had 55 submissions from seven countries. Of the 55 papers submitted, 36 were full papers, with up to 12 pages each, and 19 were extended abstracts, with up to 4 pages each. The articles submitted were carefully reviewed and selected by an international Program Comm- tee, comprising three chairs and 45 members from around the world, with the help of 21 additional reviewers. The Program Committee Chairs are very thankful to the - thors of all submitted papers, and especially to the Program Committee members and the additional reviewers, who helped select the 12 full papers and the six extended abstracts that make up this book.