{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T12:41:44Z","timestamp":1684240904207},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,8,10]],"date-time":"2020-08-10T00:00:00Z","timestamp":1597017600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["U24CA220242"],"award-info":[{"award-number":["U24CA220242"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Defining the precise location of structural variations (SVs) at single-nucleotide breakpoint resolution is a challenging problem due to large gaps in alignment. Previously, Alignment with Gap Excision (AGE) enabled us to define breakpoints of SVs at single-nucleotide resolution; however, AGE requires a vast amount of memory when aligning a pair of long sequences. To address this, we developed a memory-efficient implementation\u2014LongAGE\u2014based on the classical Hirschberg algorithm. We demonstrate an application of LongAGE for resolving breakpoints of SVs embedded into segmental duplications on Pacific Biosciences (PacBio) reads that can be longer than 10\u00a0kb. Furthermore, we observed different breakpoints for a deletion and a duplication in the same locus, providing direct evidence that such multi-allelic copy number variants (mCNVs) arise from two or more independent ancestral mutations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>LongAGE is implemented in C++ and available on Github at https:\/\/github.com\/Coaxecva\/LongAGE.<\/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\/btaa703","type":"journal-article","created":{"date-parts":[[2020,8,4]],"date-time":"2020-08-04T19:31:10Z","timestamp":1596569470000},"page":"1015-1017","source":"Crossref","is-referenced-by-count":2,"title":["LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads"],"prefix":"10.1093","volume":"37","author":[{"given":"Quang","family":"Tran","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Memphis , Memphis, TN 38152, USA"}]},{"given":"Alexej","family":"Abyzov","sequence":"additional","affiliation":[{"name":"Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic , Rochester, MN 55905, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,8,10]]},"reference":[{"key":"2023051612153251900_btaa703-B1","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1093\/bioinformatics\/btq713","article-title":"Age: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision","volume":"27","author":"Abyzov","year":"2011","journal-title":"Bioinformatics"},{"key":"2023051612153251900_btaa703-B2","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: an approach to discover, genotype, and characterize typical and atypical cnvs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res"},{"key":"2023051612153251900_btaa703-B3","doi-asserted-by":"crossref","first-page":"7256","DOI":"10.1038\/ncomms8256","article-title":"Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms","volume":"6","author":"Abyzov","year":"2015","journal-title":"Nat. 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