{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T05:28:04Z","timestamp":1768541284404,"version":"3.49.0"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>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\u20132%. 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%.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>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 <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/megasun.bch.umontreal.ca\/Software\/AutoFACT.htm\">http:\/\/megasun.bch.umontreal.ca\/Software\/AutoFACT.htm<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/1471-2105-6-151","type":"journal-article","created":{"date-parts":[[2005,6,16]],"date-time":"2005-06-16T18:13:38Z","timestamp":1118945618000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":163,"title":["AutoFACT: An Auto matic F unctional A nnotation and C lassification T ool"],"prefix":"10.1186","volume":"6","author":[{"given":"Liisa B","family":"Koski","sequence":"first","affiliation":[]},{"given":"Michael W","family":"Gray","sequence":"additional","affiliation":[]},{"given":"B Franz","family":"Lang","sequence":"additional","affiliation":[]},{"given":"Gertraud","family":"Burger","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2005,6,16]]},"reference":[{"key":"476_CR1","volume-title":"Bioinformatics","author":"LG Almeida","year":"2004","unstructured":"Almeida LG, Paixao R, Souza RC, Da Costa GC, Barrientos FJ, Dos Santos MT, De Almeida DF, Vasconcelos AT: A system for automated bacterial (genome) integrated annotation--SABIA. 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