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BMC Bioinformatics. 2005 Jun 16;6:151.

AutoFACT: an automatic functional annotation and classification tool.

Author information

1
Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, Quebec, Canada. lkoski@bch.umontreal.ca

Abstract

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.

PMID:
15960857
PMCID:
PMC1182349
DOI:
10.1186/1471-2105-6-151
[Indexed for MEDLINE]
Free PMC Article

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