AutoFACT: an automatic functional annotation and classification tool.
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%.


CONCLUSIONS
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.
Koski
Liisa B
LB
Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, Quebec, Canada. lkoski@bch.umontreal.ca
Gray
Michael W
MW
Lang
B Franz
BF
Burger
Gertraud
G
D048248:Acanthamoeba castellanii / Q000145:classification / Q000235:genetics; D000818:Animals; D019295:Computational Biology / Q000379:methods; D020451:Contig Mapping / Q000295:instrumentation / Q000379:methods; D018076:DNA, Complementary / Q000032:analysis; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D006801:Humans; D019451:Information Management / Q000379:methods*; D020407:Internet; D010802:Phylogeny; D010963:Plasmodium falciparum / Q000145:classification / Q000235:genetics; D012283:Rickettsia prowazekii / Q000145:classification / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods*; D012984:Software; D012986:Software Validation
D018076:DNA, Complementary