{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,29]],"date-time":"2023-01-29T05:22:34Z","timestamp":1674969754037},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We present PARSEC (PAtteRn Search and Contextualization), a new open source platform for guided discovery, allowing localization and biological characterization of short genomic sites in entire eukaryotic genomes. PARSEC can search for a sequence or a degenerated pattern. The retrieved set of genomic sites can be characterized in terms of (i) conservation in model organisms, (ii) genomic context (proximity to genes) and (iii) function of neighboring genes. These modules allow the user to explore, visualize, filter and extract biological knowledge from a set of short genomic regions such as transcription factor binding sites.<\/jats:p>\n               <jats:p>Availability: Web site implemented in Java, JavaScript and C++, with all major browsers supported. Freely available at lbgi.fr\/parsec. Source code is freely available at sourceforge.net\/projects\/genomicparsec.<\/jats:p>\n               <jats:p>Contact: \u00a0odile.lecompte@unistra.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt455","type":"journal-article","created":{"date-parts":[[2013,8,9]],"date-time":"2013-08-09T00:48:40Z","timestamp":1376009320000},"page":"2643-2644","source":"Crossref","is-referenced-by-count":1,"title":["PARSEC: PAtteRn SEarch and Contextualization"],"prefix":"10.1093","volume":"29","author":[{"given":"Alexis","family":"Allot","sequence":"first","affiliation":[{"name":"Laboratoire de Bioinformatique et G\u00e9nomique Int\u00e9gratives, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC) CNRS\/INSERM\/UDS, 67404, Illkirch, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yannick-No\u00ebl","family":"Anno","sequence":"additional","affiliation":[{"name":"Laboratoire de Bioinformatique et G\u00e9nomique Int\u00e9gratives, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC) CNRS\/INSERM\/UDS, 67404, Illkirch, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laetitia","family":"Poidevin","sequence":"additional","affiliation":[{"name":"Laboratoire de Bioinformatique et G\u00e9nomique Int\u00e9gratives, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC) CNRS\/INSERM\/UDS, 67404, Illkirch, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raymond","family":"Ripp","sequence":"additional","affiliation":[{"name":"Laboratoire de Bioinformatique et G\u00e9nomique Int\u00e9gratives, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC) CNRS\/INSERM\/UDS, 67404, Illkirch, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Poch","sequence":"additional","affiliation":[{"name":"Laboratoire de Bioinformatique et G\u00e9nomique Int\u00e9gratives, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC) CNRS\/INSERM\/UDS, 67404, Illkirch, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Odile","family":"Lecompte","sequence":"additional","affiliation":[{"name":"Laboratoire de Bioinformatique et G\u00e9nomique Int\u00e9gratives, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC) CNRS\/INSERM\/UDS, 67404, Illkirch, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,8,7]]},"reference":[{"key":"2023012810470729500_btt455-B1","doi-asserted-by":"crossref","first-page":"D918","DOI":"10.1093\/nar\/gkr1055","article-title":"The UCSC genome browser database: extensions and updates 2011","volume":"40","author":"Dreszer","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012810470729500_btt455-B2","doi-asserted-by":"crossref","first-page":"D84","DOI":"10.1093\/nar\/gkr991","article-title":"Ensembl 2012","volume":"40","author":"Flicek","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012810470729500_btt455-B3","doi-asserted-by":"crossref","first-page":"e579","DOI":"10.1371\/journal.pone.0000579","article-title":"Indexing strategies for rapid searches of short words in genome sequences","volume":"2","author":"Iseli","year":"2007","journal-title":"PLoS One"},{"key":"2023012810470729500_btt455-B4","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.ydbio.2010.01.027","article-title":"Retinoic acid signaling in perioptic mesenchyme represses Wnt signaling via induction of Pitx2 and Dkk2","volume":"340","author":"Kumar","year":"2010","journal-title":"Dev. 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