{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,5]],"date-time":"2024-07-05T22:41:39Z","timestamp":1720219299523},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: RNA-seq has been widely used to study the transcriptome. Comparing to microarray, sequencing-based RNA-seq is able to identify splicing variants and single nucleotide variants in one experiment simultaneously. This provides unique opportunity to detect variants that associated with aberrant splicing. Despite the popularity of RNA-seq, no bioinformatics tool has been developed to leverage this advantage to identify variants associated with aberrant splicing.<\/jats:p>\n               <jats:p>Results: We have developed PVAAS, a tool to identify single nucleotide variants that associated with aberrant alternative splicing from RNA-seq data. PVAAS works in three steps: (i) identify aberrant splicings; (ii) use user-provided variants or perform variant calling; (iii) assess the significance of association between variants and aberrant splicing events.<\/jats:p>\n               <jats:p>Availability and implementation: PVAAS is written in Python and C. Source code and a comprehensive user\u2019s manual are freely available at: http:\/\/pvaas.sourceforge.net\/.<\/jats:p>\n               <jats:p>Contact: wang.liguo@mayo.edu or kocher.jeanpierre@mayo.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv001","type":"journal-article","created":{"date-parts":[[2015,1,9]],"date-time":"2015-01-09T02:26:44Z","timestamp":1420770404000},"page":"1668-1670","source":"Crossref","is-referenced-by-count":3,"title":["PVAAS: identify variants associated with aberrant splicing from RNA-seq"],"prefix":"10.1093","volume":"31","author":[{"given":"Liguo","family":"Wang","sequence":"first","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinfu J.","family":"Nie","sequence":"additional","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Pierre A.","family":"Kocher","sequence":"additional","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,1,7]]},"reference":[{"key":"2023020115462715600_btv001-B1","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nrg775","article-title":"Listening to silence and understanding nonsense: exonic mutations that affect splicing","volume":"3","author":"Cartegni","year":"2002","journal-title":"Nat. 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Genet."},{"key":"2023020115462715600_btv001-B2","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1093\/bfgp\/elr020","article-title":"RNA splicing: disease and therapy","volume":"10","author":"Douglas","year":"2011","journal-title":"Brief Funct Genomics."},{"key":"2023020115462715600_btv001-B3","doi-asserted-by":"crossref","DOI":"10.1101\/gad.1048803","article-title":"Pre-mRNA splicing and human disease","author":"Faustino","year":"2003","journal-title":"Genes Dev"},{"key":"2023020115462715600_btv001-B4","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1016\/S0168-9525(00)02176-4","article-title":"Alternative splicing: increasing diversity in the proteomic world","volume":"17","author":"Graveley","year":"2001","journal-title":"Trends Genet."},{"key":"2023020115462715600_btv001-B5","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020115462715600_btv001-B6","doi-asserted-by":"crossref","first-page":"1900","DOI":"10.1016\/j.febslet.2005.02.047","article-title":"Are splicing mutations the most frequent cause of hereditary disease?","volume":"579","author":"L\u00f3pez-Bigas","year":"2005","journal-title":"FEBS Lett."},{"key":"2023020115462715600_btv001-B7","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.bbadis.2008.09.017","article-title":"Alternative splicing and disease","volume":"1792","author":"Tazi","year":"2009","journal-title":"Biochim. 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