{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,20]],"date-time":"2025-12-20T22:25:17Z","timestamp":1766269517673,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,3,13]],"date-time":"2020-03-13T00:00:00Z","timestamp":1584057600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["01.2.2-LMT-K-718-01-0028"],"award-info":[{"award-number":["01.2.2-LMT-K-718-01-0028"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004504","name":"Research Council of Lithuania","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004504","id-type":"DOI","asserted-by":"publisher"}]},{"name":"LMTLT"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Searching for homology in the vast amount of sequence data has a particular emphasis on its speed. We present a completely rewritten version of the sensitive homology search method COMER based on alignment of protein sequence profiles, which is capable of searching big databases even on a lightweight laptop. By harnessing the power of CUDA-enabled graphics processing units, it is up to 20 times faster than HHsearch, a state-of-the-art method using vectorized instructions on modern CPUs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>COMER2 is cross-platform open-source software available at https:\/\/sourceforge.net\/projects\/comer2 and https:\/\/github.com\/minmarg\/comer2. It can be easily installed from source code or using stand-alone installers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>mindaugas.margelevicius@bti.vu.lt<\/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\/btaa185","type":"journal-article","created":{"date-parts":[[2020,3,10]],"date-time":"2020-03-10T12:35:32Z","timestamp":1583843732000},"page":"3570-3572","source":"Crossref","is-referenced-by-count":11,"title":["COMER2: GPU-accelerated sensitive and specific homology searches"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4981-6708","authenticated-orcid":false,"given":"Mindaugas","family":"Margelevi\u010dius","sequence":"first","affiliation":[{"name":"Institute of Biotechnology , Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania"}]}],"member":"286","published-online":{"date-parts":[[2020,3,13]]},"reference":[{"key":"2023062312020207900_btaa185-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023062312020207900_btaa185-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":"2023062312020207900_btaa185-B3","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput. 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