{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T21:10:55Z","timestamp":1769202655585,"version":"3.49.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: sORF finder is a program package for identifying small open reading frames (sORFs) with high-coding potential. This application allows the identification of coding sORFs according to the nucleotide composition bias among coding sequences and the potential functional constraint at the amino acid level through evaluation of synonymous and non-synonymous substitution rates.<\/jats:p>\n               <jats:p>Availability: Online tools and source codes are freely available at http:\/\/evolver.psc.riken.jp\/<\/jats:p>\n               <jats:p>Contact: \u00a0kohanada@psc.riken.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp688","type":"journal-article","created":{"date-parts":[[2009,12,15]],"date-time":"2009-12-15T02:19:50Z","timestamp":1260843590000},"page":"399-400","source":"Crossref","is-referenced-by-count":148,"title":["sORF finder: a program package to identify small open reading frames with high coding potential"],"prefix":"10.1093","volume":"26","author":[{"given":"Kousuke","family":"Hanada","sequence":"first","affiliation":[{"name":"1 Plant Science Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 2 Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan and 3 Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA"},{"name":"1 Plant Science Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 2 Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan and 3 Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA"},{"name":"1 Plant Science Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 2 Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan and 3 Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA"}]},{"given":"Kenji","family":"Akiyama","sequence":"additional","affiliation":[{"name":"1 Plant Science Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 2 Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan and 3 Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA"}]},{"given":"Tetsuya","family":"Sakurai","sequence":"additional","affiliation":[{"name":"1 Plant Science Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 2 Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan and 3 Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA"}]},{"given":"Tetsuro","family":"Toyoda","sequence":"additional","affiliation":[{"name":"1 Plant Science Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 2 Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan and 3 Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA"}]},{"given":"Kazuo","family":"Shinozaki","sequence":"additional","affiliation":[{"name":"1 Plant Science Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 2 Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan and 3 Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA"}]},{"given":"Shin-Han","family":"Shiu","sequence":"additional","affiliation":[{"name":"1 Plant Science Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 2 Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan and 3 Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,12,14]]},"reference":[{"key":"2023012511003104600_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generate of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acid Res."},{"key":"2023012511003104600_B2","doi-asserted-by":"crossref","first-page":"2296","DOI":"10.1105\/tpc.014365","article-title":"Inflorescence deficient in abscission controls floral organ abscission in Arabidopsis and identifies a novel family of putative ligands in plants","volume":"15","author":"Butenko","year":"2003","journal-title":"Plant Cell"},{"key":"2023012511003104600_B3","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1093\/hmg\/6.10.1735","article-title":"Computational methods for the identification of genes in vertebrate genomic sequences","volume":"6","author":"Claverie","year":"1997","journal-title":"Hum. Mol. Genet."},{"key":"2023012511003104600_B4","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1104\/pp.126.3.939","article-title":"A large family of genes that share homology with CLAVATA3","volume":"126","author":"Cock","year":"2001","journal-title":"Plant Physiol."},{"key":"2023012511003104600_B5","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/nature02046","article-title":"Global analysis of protein expression in yeast","volume":"425","author":"Ghaemmaghami","year":"2003","journal-title":"Nature"},{"key":"2023012511003104600_B6","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1101\/gr.5836207","article-title":"A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and\/or under purifying selection","volume":"17","author":"Hanada","year":"2007","journal-title":"Genome Res."},{"key":"2023012511003104600_B7","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/nature02026","article-title":"Global analysis of protein localization in budding yeast","volume":"425","author":"Huh","year":"2003","journal-title":"Nature"},{"key":"2023012511003104600_B8","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1101\/gr.4355406","article-title":"Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae","volume":"16","author":"Kastenmayer","year":"2006","journal-title":"Genome Res."},{"key":"2023012511003104600_B9","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1038\/nrg1160","article-title":"Vertebrate gene predictions and the problem of large genes","volume":"4","author":"Wang","year":"2003","journal-title":"Nat. Rev. Genet."},{"key":"2023012511003104600_B10","doi-asserted-by":"crossref","first-page":"3708","DOI":"10.1073\/pnas.95.7.3708","article-title":"Positive Darwinian selection after gene duplication in primate ribonuclease genes","volume":"95","author":"Zhang","year":"1998","journal-title":"Proc. Natl Acad. Sci. USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/3\/399\/48860520\/bioinformatics_26_3_399.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/3\/399\/48860520\/bioinformatics_26_3_399.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:01:43Z","timestamp":1674644503000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/3\/399\/215607"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,12,14]]},"references-count":10,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2010,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp688","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,2,1]]},"published":{"date-parts":[[2009,12,14]]}}}