AutoFACT: An (Auto)under-barmatic (F)under-barunctional (A)under-barnnotation and (C)under-barlassification (T)under-barool

Background: Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. Results: We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it ( 1) analyzes nucleotide and protein sequence data; ( 2) determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; ( 3) assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and ( 4) generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1 - 2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. Conclusion: AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/ UNIX platforms. AutoFACT is available at http:// megasun. bch. umontreal. ca/ Software/ AutoFACT. htm.