{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T18:43:00Z","timestamp":1768070580299,"version":"3.49.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Correct annotation of genes encoding release factors in bacterial genomes is often complicated by utilization of +1 programmed ribosomal frameshifting during synthesis of release factor 2, RF2. In the absence of robust computational approaches for predicting ribosomal frameshifting, the success of proper annotation depends on annotators' familiarity with this phenomenon. Here we describe a novel computer tool that allows automatic discrimination of genes encoding class-I bacterial release factors, RF1, RF2 and RFH. Most usefully, this program identifies and automatically annotates +1 frameshifting in RF2 encoding genes. Comparison of ARFA performance with existing annotations of bacterial genomes revealed that only 20% of RF2 genes utilizing ribosomal frameshifting during their expression are annotated correctly.<\/jats:p>\n               <jats:p>Availability: The PHP based web interface of ARFA and the source code are located at<\/jats:p>\n               <jats:p>Contact: \u00a0baranov@genetics.utah.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl430","type":"journal-article","created":{"date-parts":[[2006,8,9]],"date-time":"2006-08-09T03:27:36Z","timestamp":1155094056000},"page":"2463-2465","source":"Crossref","is-referenced-by-count":32,"title":["ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting"],"prefix":"10.1093","volume":"22","author":[{"given":"Micha\u00ebl","family":"Bekaert","sequence":"first","affiliation":[{"name":"Biosciences Institute, University College Cork 1 \u00a0 1 \u00a0 \u00a0 Cork, Ireland"}]},{"given":"John F","family":"Atkins","sequence":"additional","affiliation":[{"name":"Biosciences Institute, University College Cork 1 \u00a0 1 \u00a0 \u00a0 Cork, Ireland"},{"name":"Department of Human Genetics, University of Utah 2 \u00a0 2 \u00a0 \u00a0 Salt Lake City, Utah 84112-5330, USA"}]},{"given":"Pavel V","family":"Baranov","sequence":"additional","affiliation":[{"name":"Biosciences Institute, University College Cork 1 \u00a0 1 \u00a0 \u00a0 Cork, Ireland"},{"name":"Department of Human Genetics, University of Utah 2 \u00a0 2 \u00a0 \u00a0 Salt Lake City, Utah 84112-5330, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,8,7]]},"reference":[{"key":"2023012409205781100_b1","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1093\/nar\/29.1.264","article-title":"Recode: a database of frameshifting, bypassing and codon redefinition utilized for gene expression","volume":"29","author":"Baranov","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023012409205781100_b2","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/S0378-1119(02)00423-7","article-title":"Recoding: translational bifurcations in gene expression","volume":"286","author":"Baranov","year":"2002","journal-title":"Gene"},{"key":"2023012409205781100_b3","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1093\/embo-reports\/kvf065","article-title":"Release factor 2 frameshifting sites in different bacteria","volume":"3","author":"Baranov","year":"2002","journal-title":"EMBO Rep."},{"key":"2023012409205781100_b4","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1093\/nar\/gkg024","article-title":"Recode 2003","volume":"31","author":"Baranov","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012409205781100_b5","doi-asserted-by":"crossref","DOI":"10.1186\/1745-6150-1-28","article-title":"Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons","author":"Baranov","year":"2006","journal-title":"Biology Direct"},{"key":"2023012409205781100_b6","doi-asserted-by":"crossref","first-page":"D16","DOI":"10.1093\/nar\/gkj157","article-title":"Genbank","volume":"34","author":"Benson","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012409205781100_b7","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1038\/322273a0","article-title":"Expression of peptide chain release factor 2 requires high-efficiency frameshift","volume":"322","author":"Craigen","year":"1986","journal-title":"Nature"},{"key":"2023012409205781100_b8","doi-asserted-by":"crossref","first-page":"3616","DOI":"10.1073\/pnas.82.11.3616","article-title":"Bacterial peptide chain release factors: conserved primary structure and possible frameshift regulation of release factor 2","volume":"82","author":"Craigen","year":"1985","journal-title":"Proc. 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