{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:44Z","timestamp":1772138084807,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2017,9,11]],"date-time":"2017-09-11T00:00:00Z","timestamp":1505088000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Penn Institute for Biomedical Informatics","award":["R01 AG046544"],"award-info":[{"award-number":["R01 AG046544"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Analysis of RNA sequencing (RNA-Seq) data have highlighted the fact that most genes undergo alternative splicing (AS) and that these patterns are tightly regulated. Many of these events are complex, resulting in numerous possible isoforms that quickly become difficult to visualize, interpret and experimentally validate. To address these challenges we developed MAJIQ-SPEL, a web-tool that takes as input local splicing variations (LSVs) quantified from RNA-Seq data and provides users with visualization and quantification of gene isoforms associated with those. Importantly, MAJIQ-SPEL is able to handle both classical (binary) and complex, non-binary, splicing variations. Using a matching primer design algorithm it also suggests to users possible primers for experimental validation by RT-PCR and displays those, along with the matching protein domains affected by the LSV, on UCSC Genome Browser for further downstream analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Program and code will be available at http:\/\/majiq.biociphers.org\/majiq-spel.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx565","type":"journal-article","created":{"date-parts":[[2017,9,9]],"date-time":"2017-09-09T15:08:52Z","timestamp":1504969732000},"page":"300-302","source":"Crossref","is-referenced-by-count":23,"title":["MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data"],"prefix":"10.1093","volume":"34","author":[{"given":"Christopher J","family":"Green","sequence":"first","affiliation":[{"name":"Department of Genetics, Perelman School of Medicine, Philadelphia, PA, USA"}]},{"given":"Matthew R","family":"Gazzara","sequence":"additional","affiliation":[{"name":"Department of Genetics, Perelman School of Medicine, Philadelphia, PA, USA"},{"name":"Department of Biochemistry and Biophysics, Perelman School of Medicine, Philadelphia, PA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3005-5048","authenticated-orcid":false,"given":"Yoseph","family":"Barash","sequence":"additional","affiliation":[{"name":"Department of Genetics, Perelman School of Medicine, Philadelphia, PA, USA"},{"name":"Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,9,11]]},"reference":[{"key":"2023012712225069000_btx565-B1","doi-asserted-by":"crossref","first-page":"W3","DOI":"10.1093\/nar\/gkw343","article-title":"The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update","volume":"44","author":"Afgan","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012712225069000_btx565-B2","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The pfam protein families database: towards a more sustainable future","volume":"44","author":"Finn","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012712225069000_btx565-B3","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at ucsc","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"key":"2023012712225069000_btx565-B4","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/978-1-62703-980-2_18","article-title":"Cell-based splicing of minigenes","volume":"1126","author":"Smith","year":"2014","journal-title":"Spliceosomal Pre-mRNA Splicing Methods Protoc"},{"key":"2023012712225069000_btx565-B5","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.gpb.2014.04.001","article-title":"Primerseq: design and visualization of rt-pcr primers for alternative splicing using rna-seq data","volume":"12","author":"Tokheim","year":"2014","journal-title":"Genomics Proteomics Bioinf"},{"key":"2023012712225069000_btx565-B6","doi-asserted-by":"crossref","first-page":"e11752.","DOI":"10.7554\/eLife.11752","article-title":"A new view of transcriptome complexity and regulation through the lens of local splicing variations","volume":"5","author":"Vaquero-Garcia","year":"2016","journal-title":"eLife"},{"key":"2023012712225069000_btx565-B7","doi-asserted-by":"crossref","first-page":"16219","DOI":"10.1073\/pnas.1408886111","article-title":"A circadian gene expression atlas in mammals: implications for biology and medicine","volume":"111","author":"Zhang","year":"2014","journal-title":"Proc. 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