{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T02:37:41Z","timestamp":1773283061131,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"10","funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01 GM104424 and R01 GM097358"],"award-info":[{"award-number":["R01 GM104424 and R01 GM097358"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Biological sequence databases are integral to efforts to characterize and understand biological molecules and share biological data. However, when analyzing these data, scientists are often left holding disparate biological currency\u2014molecular identifiers from different databases. For downstream applications that require converting the identifiers themselves, there are many resources available, but analyzing associated loci and variants can be cumbersome if data is not given in a form amenable to particular analyses. Here we present BISQUE, a web server and customizable command-line tool for converting molecular identifiers and their contained loci and variants between different database conventions. BISQUE uses a graph traversal algorithm to generalize the conversion process for residues in the human genome, genes, transcripts and proteins, allowing for conversion across classes of molecules and in all directions through an intuitive web interface and a URL-based web service.<\/jats:p>\n               <jats:p>Availability and implementation: BISQUE is freely available via the web using any major web browser (http:\/\/bisque.yulab.org\/). Source code is available in a public GitHub repository (https:\/\/github.com\/hyulab\/BISQUE).<\/jats:p>\n               <jats:p>Contact: \u00a0haiyuan.yu@cornell.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw043","type":"journal-article","created":{"date-parts":[[2016,2,15]],"date-time":"2016-02-15T01:09:07Z","timestamp":1455498547000},"page":"1598-1600","source":"Crossref","is-referenced-by-count":5,"title":["BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers"],"prefix":"10.1093","volume":"32","author":[{"given":"Michael J.","family":"Meyer","sequence":"first","affiliation":[{"name":"1 Department of Biological Statistics and Computational Biology,"},{"name":"2 Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA and"},{"name":"3 Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA"}]},{"given":"Philip","family":"Geske","sequence":"additional","affiliation":[{"name":"1 Department of Biological Statistics and Computational Biology,"},{"name":"2 Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA and"}]},{"given":"Haiyuan","family":"Yu","sequence":"additional","affiliation":[{"name":"1 Department of Biological Statistics and Computational Biology,"},{"name":"2 Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA and"}]}],"member":"286","published-online":{"date-parts":[[2016,1,23]]},"reference":[{"key":"2023020112260693700_btw043-B1","doi-asserted-by":"crossref","first-page":"D30","DOI":"10.1093\/nar\/gku1216","article-title":"GenBank","volume":"43","author":"Benson","year":"2015","journal-title":"Nucleic. Acids. Res"},{"key":"2023020112260693700_btw043-B2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic. Acids. Res"},{"key":"2023020112260693700_btw043-B3","doi-asserted-by":"crossref","first-page":"D662","DOI":"10.1093\/nar\/gku1010","article-title":"Ensembl 2015","volume":"43","author":"Cunningham","year":"2015","journal-title":"Nucleic. Acids. Res"},{"key":"2023020112260693700_btw043-B4","doi-asserted-by":"crossref","first-page":"D1079","DOI":"10.1093\/nar\/gku1071","article-title":"Genenames.org: the HGNC resources in 2015","volume":"43","author":"Gray","year":"2015","journal-title":"Nucleic. Acids. 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Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/10\/1598\/49019333\/bioinformatics_32_10_1598.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/10\/1598\/49019333\/bioinformatics_32_10_1598.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:30:28Z","timestamp":1675290628000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/10\/1598\/1743453"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,1,23]]},"references-count":8,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2016,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw043","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,5,15]]},"published":{"date-parts":[[2016,1,23]]}}}