{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T07:26:51Z","timestamp":1784359611905,"version":"3.55.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate-pair read pairs to a reference genome is a challenging and time-consuming process for most next-generation sequencing alignment programs. Large insert sizes, introduction of library preparation protocol artifacts (biotin junction reads, paired-end read contamination, chimeras, etc.) and presence of structural variant breakpoints within reads increase mapping and alignment complexity. We describe an algorithm that is up to 20 times faster and 25% more accurate than popular next-generation sequencing alignment programs when processing mate pair sequencing.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/bioinformaticstools.mayo.edu\/research\/bima\/<\/jats:p>\n               <jats:p>Contact: \u00a0vasm@mayo.edu or vasmatzis.george@mayo.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu078","type":"journal-article","created":{"date-parts":[[2014,2,14]],"date-time":"2014-02-14T03:19:10Z","timestamp":1392347950000},"page":"1627-1629","source":"Crossref","is-referenced-by-count":78,"title":["BIMA V3: an aligner customized for mate pair library sequencing"],"prefix":"10.1093","volume":"30","author":[{"given":"Travis M.","family":"Drucker","sequence":"first","affiliation":[{"name":"1 Department of Information Technology, MN 55905, 2Department of Molecular Medicine, 3Department of Laboratory Medicine and Pathology and 4Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah H.","family":"Johnson","sequence":"additional","affiliation":[{"name":"1 Department of Information Technology, MN 55905, 2Department of Molecular Medicine, 3Department of Laboratory Medicine and Pathology and 4Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen J.","family":"Murphy","sequence":"additional","affiliation":[{"name":"1 Department of Information Technology, MN 55905, 2Department of Molecular Medicine, 3Department of Laboratory Medicine and Pathology and 4Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kendall W.","family":"Cradic","sequence":"additional","affiliation":[{"name":"1 Department of Information Technology, MN 55905, 2Department of Molecular Medicine, 3Department of Laboratory Medicine and Pathology and 4Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Terry M.","family":"Therneau","sequence":"additional","affiliation":[{"name":"1 Department of Information Technology, MN 55905, 2Department of Molecular Medicine, 3Department of Laboratory Medicine and Pathology and 4Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Vasmatzis","sequence":"additional","affiliation":[{"name":"1 Department of Information Technology, MN 55905, 2Department of Molecular Medicine, 3Department of Laboratory Medicine and Pathology and 4Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,2,12]]},"reference":[{"key":"2023012710551462800_btu078-B1","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1182\/blood-2010-08-303305","article-title":"Discovery of recurrent t(6;7)(p25.3;q32.3) translocations in ALK-negative anaplastic large cell lymphomas by massively parallel genomic sequencing","volume":"117","author":"Feldman","year":"2011","journal-title":"Blood"},{"key":"2023012710551462800_btu078-B2","first-page":"656","article-title":"BLAT\u2014the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023012710551462800_btu078-B3","doi-asserted-by":"crossref","first-page":"3275","DOI":"10.1158\/0008-5472.CAN-12-2803","article-title":"Lineage relationship of Gleason patterns in Gleason score 7 prostate cancer","volume":"73","author":"Kovtun","year":"2013","journal-title":"Cancer Res."},{"key":"2023012710551462800_btu078-B4","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012710551462800_btu078-B5","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1093\/bib\/bbq015","article-title":"A survey of sequence alignment algorithms for next-generation sequencing","volume":"11","author":"Li","year":"2010","journal-title":"Brief. 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