{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T14:17:00Z","timestamp":1768918620006,"version":"3.49.0"},"reference-count":19,"publisher":"World Scientific Pub Co Pte Ltd","issue":"04","funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["61763031"],"award-info":[{"award-number":["61763031"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004479","name":"Natural Science Foundation of Jiangxi Province","doi-asserted-by":"crossref","award":["20202BAB202018"],"award-info":[{"award-number":["20202BAB202018"]}],"id":[{"id":"10.13039\/501100004479","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2022,8]]},"abstract":"<jats:p> High-quality multiple sequence alignments can provide insights into the architecture and function of protein families. The existing MSA tools often generate results inconsistent with biological distribution of conserved regions because of positioning amino acid residues and gaps only by symbols. We propose RPfam, a refiner towards curated-like MSAs for modeling the protein families in the Pfam database. RPfam refines the automatic alignments via scoring alignments based on the PFASUM matrix, restricting realignments within badly aligned blocks, optimizing the block scores by dynamic programming, and running refinements iteratively using the Simulated Annealing algorithm. Experiments show RPfam effectively refined the alignments produced by the MSA tools ClustalO and Muscle with reference to the curated seed alignments of the Pfam protein families. Especially RPfam improved the quality of the ClustalO alignments by 4.4% and the Muscle alignments by 2.8% on the gp32 DNA binding protein-like family. Supplementary Table is available at http:\/\/www.worldscinet.com\/jbcb\/ . <\/jats:p>","DOI":"10.1142\/s0219720022400029","type":"journal-article","created":{"date-parts":[[2022,4,17]],"date-time":"2022-04-17T15:41:21Z","timestamp":1650210081000},"source":"Crossref","is-referenced-by-count":5,"title":["RPfam: A refiner towards curated-like multiple sequence alignments of the Pfam protein families"],"prefix":"10.1142","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8051-8955","authenticated-orcid":false,"given":"Qingting","family":"Wei","sequence":"first","affiliation":[{"name":"School of Software, Nanchang University, Nanchang 330047, Jiangxi Province, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong","family":"Zou","sequence":"additional","affiliation":[{"name":"Jiangxi Provincial Armed Force Unit Hospital, Nanchang 330043, Jiangxi Province, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cuncong","family":"Zhong","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence, KS 66045, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianfeng","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Software, Nanchang University, Nanchang 330047, Jiangxi Province, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2022,4,14]]},"reference":[{"key":"S0219720022400029BIB001","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-7-484"},{"key":"S0219720022400029BIB002","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2018.0031"},{"key":"S0219720022400029BIB003","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1748-7188-9-1","volume":"9","author":"Pais SM","year":"2014","journal-title":"Algor Mol Biol"},{"key":"S0219720022400029BIB004","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2006.04.004"},{"key":"S0219720022400029BIB005","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa913"},{"key":"S0219720022400029BIB006","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.4042"},{"key":"S0219720022400029BIB007","doi-asserted-by":"publisher","DOI":"10.1038\/msb.2011.75"},{"key":"S0219720022400029BIB008","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh340"},{"key":"S0219720022400029BIB009","first-page":"772","volume":"30","author":"Katoh K","year":"2013","journal-title":"Mol Syst Biol"},{"key":"S0219720022400029BIB010","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn1006"},{"key":"S0219720022400029BIB011","doi-asserted-by":"publisher","DOI":"10.1038\/srep33964"},{"key":"S0219720022400029BIB012","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-7-499"},{"key":"S0219720022400029BIB013","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg133"},{"key":"S0219720022400029BIB014","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/22.22.4673"},{"key":"S0219720022400029BIB015","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl274"},{"key":"S0219720022400029BIB016","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-210"},{"key":"S0219720022400029BIB017","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp651"},{"key":"S0219720022400029BIB018","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-017-1703-z"},{"key":"S0219720022400029BIB019","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-24974-7_7"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720022400029","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,11]],"date-time":"2022-09-11T03:21:29Z","timestamp":1662866489000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/10.1142\/S0219720022400029"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,4,14]]},"references-count":19,"journal-issue":{"issue":"04","published-print":{"date-parts":[[2022,8]]}},"alternative-id":["10.1142\/S0219720022400029"],"URL":"https:\/\/doi.org\/10.1142\/s0219720022400029","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,4,14]]},"article-number":"2240002"}}