{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T19:00:17Z","timestamp":1772910017951,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM's accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be.<\/jats:p>\n               <jats:p>Results: In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that\u2014unlike family-specific solutions\u2014can scale to hundreds of ncRNA families.<\/jats:p>\n               <jats:p>Availability: The source code is available under GNU Public License at the supplementary web site.<\/jats:p>\n               <jats:p>Contact: \u00a0zasha@cs.washington.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0 (Technical details, results, C++ code)<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti743","type":"journal-article","created":{"date-parts":[[2005,11,3]],"date-time":"2005-11-03T01:13:48Z","timestamp":1130980428000},"page":"35-39","source":"Crossref","is-referenced-by-count":72,"title":["Sequence-based heuristics for faster annotation of non-coding RNA families"],"prefix":"10.1093","volume":"22","author":[{"given":"Zasha","family":"Weinberg","sequence":"first","affiliation":[{"name":"Department of Computer Science & Engineering 1 \u00a0 1 \u00a0 \u00a0 Seattle, WA 98195, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Walter L.","family":"Ruzzo","sequence":"additional","affiliation":[{"name":"Department of Computer Science & Engineering 1 \u00a0 1 \u00a0 \u00a0 Seattle, WA 98195, USA"},{"name":"Department of Genome Sciences, University of Washington 2 \u00a0 2 \u00a0 \u00a0 Seattle, WA 98195, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2005,11,2]]},"reference":[{"key":"2023012408311579000_b1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012408311579000_b2","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511790492","author":"Durbin","year":"1998","journal-title":"Biological Sequence Analysis"},{"key":"2023012408311579000_b3","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/S0092-8674(02)00727-4","article-title":"Computational genomics of noncoding RNA genes","volume":"109","author":"Eddy","year":"2002","journal-title":"Cell"},{"key":"2023012408311579000_b4","doi-asserted-by":"crossref","first-page":"2079","DOI":"10.1093\/nar\/22.11.2079","article-title":"RNA sequence analysis using covariance models","volume":"22","author":"Eddy","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"2023012408311579000_b5","doi-asserted-by":"crossref","first-page":"D121","DOI":"10.1093\/nar\/gki081","article-title":"Rfam: annotating non-coding RNAs in complete genomes","volume":"33","author":"Griffiths-Jones","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012408311579000_b6","doi-asserted-by":"crossref","first-page":"2283","DOI":"10.1126\/science.298.5602.2283","article-title":"Breakthrough of the year","volume":"298","author":"Kennedy","year":"2002","journal-title":"Science"},{"key":"2023012408311579000_b7","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1471-2105-4-44","article-title":"RSEARCH: finding homologs of single structured RNA sequences","volume":"4","author":"Klein","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2023012408311579000_b8","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1126\/science.1083516","volume":"300","author":"Kryukov","year":"2003","journal-title":"Science"},{"key":"2023012408311579000_b9","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012408311579000_b10","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1126\/science.1100829","article-title":"A glycine-dependent riboswitch that uses cooperative binding to control gene expression","volume":"306","author":"Mandal","year":"2004","journal-title":"Science"},{"key":"2023012408311579000_b11","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/S0001-2998(78)80014-2","article-title":"Basic principles of ROC analysis","volume":"8","author":"Metz","year":"1978","journal-title":"Semin. 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