{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T10:11:25Z","timestamp":1675332685946},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Interactive examination of RNA multiple alignments for covariant mutations is a useful step in non-coding RNA sequence analysis. We present three parallel implementations of an RNA visualization metaphor: Colorstock, a command-line script using ANSI terminal color; SScolor, a Perl script that generates static HTML pages; and Rat\u00f3n, an AJAX web application generating dynamic HTML. Each tool can be used to color RNA alignments by secondary structure and to visually highlight compensatory mutations in stems.<\/jats:p>\n               <jats:p>Availability: All source code is freely available under the GPL. The source code can be downloaded and a prototype of Rat\u00f3n can be accessed at http:\/\/biowiki.org\/RnaAlignmentViewers<\/jats:p>\n               <jats:p>Contact: \u00a0ihh@berkeley.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm635","type":"journal-article","created":{"date-parts":[[2008,1,25]],"date-time":"2008-01-25T01:24:39Z","timestamp":1201224279000},"page":"579-580","source":"Crossref","is-referenced-by-count":3,"title":["Colorstock, SScolor, Rat\u00f3n: RNA alignment visualization tools"],"prefix":"10.1093","volume":"24","author":[{"given":"Yuri R.","family":"Benda\u00f1a","sequence":"first","affiliation":[{"name":"Department of Bioengineering, UC Berkeley, Berkeley, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian H.","family":"Holmes","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, UC Berkeley, Berkeley, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,1,24]]},"reference":[{"key":"2023020209510232300_B1","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1242\/dev.002006","article-title":"The regulation of genes and genomes by small RNAs","volume":"134","author":"Ambros","year":"2007","journal-title":"Development"},{"key":"2023020209510232300_B2","article-title":"An XRATE ncRNA pipeline","author":"Bradley","year":"2007"},{"key":"2023020209510232300_B3","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1038\/nature03195","article-title":"Natural and engineered nucleic acids as tools to explore biology","volume":"432","author":"Breaker","year":"2004","journal-title":"Nature"},{"key":"2023020209510232300_B4","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1093\/bioinformatics\/bth489","article-title":"RALEE\u2013RNA ALignment editor in Emacs","volume":"21","author":"Griffiths-Jones","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020209510232300_B5","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/nar\/gkg006","article-title":"Rfam: an RNA family database","volume":"31","author":"Griffiths-Jones","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2023020209510232300_B6","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1186\/1471-2105-7-428","article-title":"XRate: a fast prototyping, training and annotation tool for phylo-grammars","volume":"7","author":"Klosterman","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023020209510232300_B7","doi-asserted-by":"crossref","first-page":"e33","DOI":"10.1371\/journal.pcbi.0020033","article-title":"Identification and classification of conserved RNA secondary structures in the human genome","volume":"2","author":"Pedersen","year":"2007","journal-title":"PLoS Computational Biology"},{"key":"2023020209510232300_B8","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1101\/gr.6406307","article-title":"Raising the estimate of functional human sequences","volume":"17","author":"Pheasant","year":"2007","journal-title":"Genome Res"},{"key":"2023020209510232300_B9","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1016\/S0960-9822(01)00401-8","article-title":"Computational identification of noncoding RNAs in E. coli by comparative genomics","volume":"11","author":"Rivas","year":"2001","journal-title":"Curr. 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