{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:43:30Z","timestamp":1761745410270,"version":"3.37.3"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2021,1,18]],"date-time":"2021-01-18T00:00:00Z","timestamp":1610928000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100005289","name":"National Institute of Justice, Office of Justice Programs","doi-asserted-by":"crossref","award":["2018-DU-BX-0177"],"award-info":[{"award-number":["2018-DU-BX-0177"]}],"id":[{"id":"10.13039\/100005289","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000074","name":"U.S. Department of Justice","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000074","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000074","name":"U.S. Department of Justice","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000074","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Current read-mapping software uses a singular specification of alignment parameters with respect to the reference. In the presence of varying reference structures (such as the repetitive regions of the human genome), alignments can be improved if those parameters are allowed vary.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To that end, the C++ program ProDerAl was written to refine previously generated alignments using varying parameters for these problematic regions. Synthetic benchmarks show that this realignment can result in an order of magnitude fewer misaligned bases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>*Nix users can retrieve the source from GitHub (https:\/\/github.com\/Benjamin-Crysup\/proderal.git). Windows binary available at https:\/\/github.com\/Benjamin-Crysup\/proderal\/releases\/download\/v1.1\/proderal.zip.<\/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\/btab008","type":"journal-article","created":{"date-parts":[[2021,1,4]],"date-time":"2021-01-04T20:35:40Z","timestamp":1609792540000},"page":"2479-2480","source":"Crossref","is-referenced-by-count":3,"title":["ProDerAl: reference position dependent alignment"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2593-2280","authenticated-orcid":false,"given":"Benjamin","family":"Crysup","sequence":"first","affiliation":[{"name":"Center for Human Identification, University of North Texas , Fort Worth, TX 76107, USA"}]},{"given":"Bruce","family":"Budowle","sequence":"additional","affiliation":[{"name":"Center for Human Identification, University of North Texas , Fort Worth, TX 76107, USA"}]},{"given":"August E","family":"Woerner","sequence":"additional","affiliation":[{"name":"Center for Human Identification, University of North Texas , Fort Worth, TX 76107, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,1,18]]},"reference":[{"key":"2023051609055366400_btab008-B1","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1101\/gr.210500.116","article-title":"A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree","volume":"27","author":"Eberle","year":"2017","journal-title":"Genome Res"},{"key":"2023051609055366400_btab008-B2","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1038\/nrg1348","article-title":"Microsatellites: simple sequences with complex evolution","volume":"5","author":"Ellegren","year":"2004","journal-title":"Nat. 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