{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T11:03:36Z","timestamp":1787828616966,"version":"build-2784847793"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2018,7,13]],"date-time":"2018-07-13T00:00:00Z","timestamp":1531440000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["ERC-StG-LS2-637591"],"award-info":[{"award-number":["ERC-StG-LS2-637591"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["ERC-AdG-MASCP-670146"],"award-info":[{"award-number":["ERC-AdG-MASCP-670146"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Spanish Ministry of Economy and Competitiveness","award":["BFU2014-55076-P"],"award-info":[{"award-number":["BFU2014-55076-P"]}]},{"name":"Spanish Ministry of Economy and Competitiveness","award":["BFU2014-55058-P"],"award-info":[{"award-number":["BFU2014-55058-P"]}]},{"name":"EMBL partnership","award":["SEV-2012-0208"],"award-info":[{"award-number":["SEV-2012-0208"]}]},{"name":"Excelencia Severo Ochoa and CERCA"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"abstract":"Abstract<\/jats:title>\n \n Summary<\/jats:title>\n Tracking thousands of alternative splicing (AS) events genome-wide makes their downstream analysis computationally challenging and laborious. Here, we present Matt, the first UNIX command-line toolkit with focus on high-level AS analyses. With 50 commands it facilitates computational AS analyses by (i) expediting repetitive data-preparation tasks, (ii) offering routine high-level analyses, including the extraction of exon\/intron features, discriminative feature detection, motif enrichment analysis, and the generation of motif RNA-maps, (iii) improving reproducibility by documenting all analysis steps and (iv) accelerating the implementation of own analysis pipelines by offering users to exploit its modular functionality.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n matt.crg.eu under GNU LGPLv3, together with comprehensive documentation and application examples. Matt is implemented in Perl and R, invokes pdfLATEX and depends only on Perl Core modules\/the R Base package simplifying its installation.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty606","type":"journal-article","created":{"date-parts":[[2018,7,13]],"date-time":"2018-07-13T07:29:23Z","timestamp":1531466963000},"page":"130-132","source":"Crossref","is-referenced-by-count":80,"title":["Matt<\/i>\n : Unix tools for alternative splicing analysis"],"prefix":"10.1093","volume":"35","author":[{"given":"Andr\u00e9","family":"Gohr","sequence":"first","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel","family":"Irimia","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain"},{"name":"Universitat Pompeu Fabra (UPF), Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,7,13]]},"reference":[{"key":"2023013107195174900_bty606-B1","doi-asserted-by":"crossref","first-page":"R20","DOI":"10.1186\/gb-2014-15-1-r20","article-title":"RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing","volume":"15","author":"Cereda","year":"2014","journal-title":"Genome Biol."},{"key":"2023013107195174900_bty606-B2","doi-asserted-by":"crossref","first-page":"e1001016","DOI":"10.1371\/journal.pcbi.1001016","article-title":"Genome-wide association between branch point properties and alternative splicing","volume":"6","author":"Corvelo","year":"2010","journal-title":"PLoS Comput. 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Comput. 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