{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:13Z","timestamp":1674710413178},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1721,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,15]]},"abstract":"Abstract<\/jats:title>\n Motivation: The prediction and annotation of the genomic regions involved in gene expression has been largely explored. Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding sites (TFBSs) largely unexplored and with important quantitative and qualitative methodological gaps.<\/jats:p>\n Results: We have developed ReLA (for REgulatory region Local Alignment tool), a unique tool optimized with the Smith\u2013Waterman algorithm that allows local searches of conserved TFBS clusters and the detection of regulatory regions proximal to genes and enhancer regions. ReLA's performance shows specificities of 81 and 50% when tested on experimentally validated proximal regulatory regions and enhancers, respectively.<\/jats:p>\n Availability: The source code of ReLA's is freely available and can be remotely used through our web server under http:\/\/www.bsc.es\/cg\/rela.<\/jats:p>\n Contact: \u00a0david.torrents@bsc.es<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts024","type":"journal-article","created":{"date-parts":[[2012,1,18]],"date-time":"2012-01-18T02:33:15Z","timestamp":1326853995000},"page":"763-770","source":"Crossref","is-referenced-by-count":11,"title":["ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites"],"prefix":"10.1093","volume":"28","author":[{"given":"Santi","family":"Gonz\u00e1lez","sequence":"first","affiliation":[{"name":"1 Joint IRB-BSC program on Computational Biology, BSC c\/ Jordi Girona 29, 2Department of Computer Architecture, Campus Nord UPC D6-117, Jordi Girona 1-3, 08034 Barcelona, 3Computational Bioinformatics, National Institute of Bioinformatics, 4Departament de Gen\u00e8tica i Institut de Biomedicina (IBUB), Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Catalonia and 5Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) Pg. Llu\u00eds Companys 23, 08010 Barcelona, Catalonia"}]},{"given":"B\u00e0rbara","family":"Montserrat-Sent\u00eds","sequence":"additional","affiliation":[{"name":"1 Joint IRB-BSC program on Computational Biology, BSC c\/ Jordi Girona 29, 2Department of Computer Architecture, Campus Nord UPC D6-117, Jordi Girona 1-3, 08034 Barcelona, 3Computational Bioinformatics, National Institute of Bioinformatics, 4Departament de Gen\u00e8tica i Institut de Biomedicina (IBUB), Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Catalonia and 5Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) Pg. Llu\u00eds Companys 23, 08010 Barcelona, Catalonia"}]},{"given":"Friman","family":"S\u00e1nchez","sequence":"additional","affiliation":[{"name":"1 Joint IRB-BSC program on Computational Biology, BSC c\/ Jordi Girona 29, 2Department of Computer Architecture, Campus Nord UPC D6-117, Jordi Girona 1-3, 08034 Barcelona, 3Computational Bioinformatics, National Institute of Bioinformatics, 4Departament de Gen\u00e8tica i Institut de Biomedicina (IBUB), Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Catalonia and 5Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) Pg. Llu\u00eds Companys 23, 08010 Barcelona, Catalonia"}]},{"given":"Montserrat","family":"Puiggr\u00f2s","sequence":"additional","affiliation":[{"name":"1 Joint IRB-BSC program on Computational Biology, BSC c\/ Jordi Girona 29, 2Department of Computer Architecture, Campus Nord UPC D6-117, Jordi Girona 1-3, 08034 Barcelona, 3Computational Bioinformatics, National Institute of Bioinformatics, 4Departament de Gen\u00e8tica i Institut de Biomedicina (IBUB), Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Catalonia and 5Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) Pg. Llu\u00eds Companys 23, 08010 Barcelona, Catalonia"},{"name":"1 Joint IRB-BSC program on Computational Biology, BSC c\/ Jordi Girona 29, 2Department of Computer Architecture, Campus Nord UPC D6-117, Jordi Girona 1-3, 08034 Barcelona, 3Computational Bioinformatics, National Institute of Bioinformatics, 4Departament de Gen\u00e8tica i Institut de Biomedicina (IBUB), Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Catalonia and 5Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) Pg. Llu\u00eds Companys 23, 08010 Barcelona, Catalonia"}]},{"given":"Enrique","family":"Blanco","sequence":"additional","affiliation":[{"name":"1 Joint IRB-BSC program on Computational Biology, BSC c\/ Jordi Girona 29, 2Department of Computer Architecture, Campus Nord UPC D6-117, Jordi Girona 1-3, 08034 Barcelona, 3Computational Bioinformatics, National Institute of Bioinformatics, 4Departament de Gen\u00e8tica i Institut de Biomedicina (IBUB), Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Catalonia and 5Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) Pg. Llu\u00eds Companys 23, 08010 Barcelona, Catalonia"}]},{"given":"Alex","family":"Ramirez","sequence":"additional","affiliation":[{"name":"1 Joint IRB-BSC program on Computational Biology, BSC c\/ Jordi Girona 29, 2Department of Computer Architecture, Campus Nord UPC D6-117, Jordi Girona 1-3, 08034 Barcelona, 3Computational Bioinformatics, National Institute of Bioinformatics, 4Departament de Gen\u00e8tica i Institut de Biomedicina (IBUB), Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Catalonia and 5Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) Pg. Llu\u00eds Companys 23, 08010 Barcelona, Catalonia"}]},{"given":"David","family":"Torrents","sequence":"additional","affiliation":[{"name":"1 Joint IRB-BSC program on Computational Biology, BSC c\/ Jordi Girona 29, 2Department of Computer Architecture, Campus Nord UPC D6-117, Jordi Girona 1-3, 08034 Barcelona, 3Computational Bioinformatics, National Institute of Bioinformatics, 4Departament de Gen\u00e8tica i Institut de Biomedicina (IBUB), Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Catalonia and 5Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) Pg. Llu\u00eds Companys 23, 08010 Barcelona, Catalonia"},{"name":"1 Joint IRB-BSC program on Computational Biology, BSC c\/ Jordi Girona 29, 2Department of Computer Architecture, Campus Nord UPC D6-117, Jordi Girona 1-3, 08034 Barcelona, 3Computational Bioinformatics, National Institute of Bioinformatics, 4Departament de Gen\u00e8tica i Institut de Biomedicina (IBUB), Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Catalonia and 5Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) Pg. Llu\u00eds Companys 23, 08010 Barcelona, Catalonia"}]}],"member":"286","published-online":{"date-parts":[[2012,1,16]]},"reference":[{"key":"2023012512200973600_B1","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1101\/gr.6991408","article-title":"Generic eukaryotic core promoter prediction using structural features of DNA","volume":"18","author":"Abeel","year":"2008","journal-title":"Genome Res."},{"key":"2023012512200973600_B2","doi-asserted-by":"crossref","first-page":"i313","DOI":"10.1093\/bioinformatics\/btp191","article-title":"Toward a gold standard for promoter prediction evaluation","volume":"25","author":"Abeel","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512200973600_B3","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":"2023012512200973600_B4","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1002\/jcb.20352","article-title":"Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?","volume":"94","author":"Arnosti","year":"2005","journal-title":"J. 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