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Open Access Software

AutoFACT: An Automatic Functional Annotation and Classification Tool

Liisa B Koski1*, Michael W Gray2, B Franz Lang1 and Gertraud Burger1

Author Affiliations

1 Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, Quebec, Canada

2 Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada

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BMC Bioinformatics 2005, 6:151  doi:10.1186/1471-2105-6-151

Published: 16 June 2005



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.


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%.


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 webcite.