{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T00:29:17Z","timestamp":1748564957704},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,1,30]],"date-time":"2018-01-30T00:00:00Z","timestamp":1517270400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Protein sequence alignment forms the basis for comparative modeling, the most reliable approach to protein structure prediction, among many other applications. Alignment between sequence families, or profile\u2013profile alignment, represents one of the most, if not the most, sensitive means for homology detection but still necessitates improvement. We aim at improving the quality of profile\u2013profile alignments and the sensitivity induced by them by refining profile\u2013profile substitution scores.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed a new score that represents an additional component of profile\u2013profile substitution scores. A comprehensive evaluation shows that the new add-on score statistically significantly improves both the sensitivity and the alignment quality of the COMER method. We discuss why the score leads to the improvement and its almost optimal computational complexity that makes it easily implementable in any profile\u2013profile alignment method.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>An implementation of the add-on score in the open-source COMER software and data are available at https:\/\/sourceforge.net\/projects\/comer. The COMER software is also available on Github at https:\/\/github.com\/minmarg\/comer and as a Docker image (minmar\/comer).<\/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\/bty048","type":"journal-article","created":{"date-parts":[[2018,1,29]],"date-time":"2018-01-29T12:10:57Z","timestamp":1517227857000},"page":"2037-2045","source":"Crossref","is-referenced-by-count":6,"title":["A low-complexity add-on score for protein remote homology search with COMER"],"prefix":"10.1093","volume":"34","author":[{"given":"Mindaugas","family":"Margelevi\u010dius","sequence":"first","affiliation":[{"name":"Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania"}]}],"member":"286","published-online":{"date-parts":[[2018,1,30]]},"reference":[{"key":"2023012713393468000_bty048-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":"2023012713393468000_bty048-B2","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1214\/aoap\/1177005208","article-title":"A phase transition for the score in matching random sequences allowing deletions","volume":"4","author":"Arratia","year":"1994","journal-title":"Ann. 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