{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,8,27]],"date-time":"2023-08-27T11:53:38Z","timestamp":1693137218463},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: RNATOPS-W is a web server to search sequences for RNA secondary structures including pseudoknots. The server accepts an annotated RNA multiple structural alignment as a structural profile and genomic or other sequences to search. It is built upon RNATOPS, a command line C++software package for the same purpose, in which filters to speed up search are manually selected. RNATOPS-W improves upon RNATOPS by adding the function of automatic selection of a hidden Markov model (HMM) filter and also a friendly user interface for selection of a substructure filter by the user. In addition, RNATOPS-W complements existing RNA secondary structure search web servers that either use built-in structure profiles or are not able to detect pseudoknots. RNATOPS-W inherits the efficiency of RNATOPS in detecting large, complex RNA structures.<\/jats:p>\n               <jats:p>Availability: The web server RNATOPS-W is available at the web site www.uga.edu\/RNA-Informatics\/?f=software&amp;p=RNATOPS-w. The underlying search program RNATOPS can be downloaded at www.uga.edu\/RNA-Informatics\/?f=software&amp;p=RNATOPS.<\/jats:p>\n               <jats:p>Contact: \u00a0cai@cs.uga.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp095","type":"journal-article","created":{"date-parts":[[2009,3,7]],"date-time":"2009-03-07T01:24:42Z","timestamp":1236389082000},"page":"1080-1081","source":"Crossref","is-referenced-by-count":1,"title":["RNATOPS-W: a web server for RNA structure searches of genomes"],"prefix":"10.1093","volume":"25","author":[{"given":"Yingfeng","family":"Wang","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, 2Department of Plant Biology and 3Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhibin","family":"Huang","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2Department of Plant Biology and 3Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yong","family":"Wu","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2Department of Plant Biology and 3Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Russell L.","family":"Malmberg","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2Department of Plant Biology and 3Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA"},{"name":"1 Department of Computer Science, 2Department of Plant Biology and 3Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liming","family":"Cai","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2Department of Plant Biology and 3Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA"},{"name":"1 Department of Computer Science, 2Department of Plant Biology and 3Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,3,5]]},"reference":[{"key":"2023051607021130500_B1","first-page":"52","article-title":"FastR: fast database search tool for non-coding RNA","volume-title":"In Proceedings of the 3rd IEEE Computational Systems Bioinformatics Conference","author":"Bafna","year":"2004"},{"key":"2023051607021130500_B2","doi-asserted-by":"crossref","first-page":"1875","DOI":"10.1093\/bioinformatics\/btm270","article-title":"Predicting functionally important residues from sequence conservation","volume":"15","author":"Capra","year":"2007","journal-title":"Bioinformatics"},{"key":"2023051607021130500_B3","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1146\/annurev.genom.8.080706.092419","article-title":"Annotating noncoding RNA genes","volume":"8","author":"Griffiths-Jones","year":"2007","journal-title":"Ann. 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