{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,4,17]],"date-time":"2023-04-17T01:25:14Z","timestamp":1681694714357},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: One approach to infer functions of new proteins from their homologs utilizes visualization of an all-against-all pairwise similarity network (A2ApsN) that exploits the speed of BLAST and avoids the complexity of multiple sequence alignment. However, identifying functions of the protein clusters in A2ApsN is never trivial, due to a lack of linking characterized proteins to their relevant information in current software packages. Given the database errors introduced by automatic annotation transfer, functional deduction should be made from proteins with experimental studies, i.e. \u2018reference proteins\u2019. Here, we present a web server, termed Pclust, which provides a user-friendly interface to visualize the A2ApsN, placing emphasis on such \u2018reference proteins\u2019 and providing access to their full information in source databases, e.g. articles in PubMed. The identification of \u2018reference proteins\u2019 and the ease of cross-database linkage will facilitate understanding the functions of protein clusters in the network, thus promoting interpretation of proteins of interest.<\/jats:p>\n               <jats:p>Availability: The Pclust server is freely available at http:\/\/prodata.swmed.edu\/pclust<\/jats:p>\n               <jats:p>Contact: \u00a0grishin@chop.swmed.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt451","type":"journal-article","created":{"date-parts":[[2013,8,6]],"date-time":"2013-08-06T05:30:10Z","timestamp":1375767010000},"page":"2647-2648","source":"Crossref","is-referenced-by-count":7,"title":["Pclust: protein network visualization highlighting experimental data"],"prefix":"10.1093","volume":"29","author":[{"given":"Wenlin","family":"Li","sequence":"first","affiliation":[{"name":"1 Departments of Biophysics and Biochemistry and 2Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA"}]},{"given":"Lisa N.","family":"Kinch","sequence":"additional","affiliation":[{"name":"1 Departments of Biophysics and Biochemistry and 2Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA"}]},{"given":"Nick V.","family":"Grishin","sequence":"additional","affiliation":[{"name":"1 Departments of Biophysics and Biochemistry and 2Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA"},{"name":"1 Departments of Biophysics and Biochemistry and 2Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,8,5]]},"reference":[{"key":"2023012810465063000_btt451-B1","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/1471-2105-14-S1-S1","article-title":"Visualization of protein interaction networks: problems and solutions","volume":"14","author":"Agapito","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023012810465063000_btt451-B2","doi-asserted-by":"crossref","first-page":"e4345","DOI":"10.1371\/journal.pone.0004345","article-title":"Using sequence similarity networks for visualization of relationships across diverse protein superfamilies","volume":"4","author":"Atkinson","year":"2009","journal-title":"PLoS One"},{"key":"2023012810465063000_btt451-B3","doi-asserted-by":"crossref","first-page":"2845","DOI":"10.1093\/bioinformatics\/bts532","article-title":"Pythoscape: a framework for generation of large protein similarity networks","volume":"28","author":"Barber","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012810465063000_btt451-B4","doi-asserted-by":"crossref","first-page":"2086","DOI":"10.1002\/prot.23029","article-title":"Analysis of protein function and its prediction from amino acid sequence","volume":"79","author":"Clark","year":"2011","journal-title":"Proteins"},{"key":"2023012810465063000_btt451-B5","doi-asserted-by":"crossref","first-page":"3702","DOI":"10.1093\/bioinformatics\/bth444","article-title":"CLANS: a Java application for visualizing protein families based on pairwise similarity","volume":"20","author":"Frickey","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012810465063000_btt451-B6","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012810465063000_btt451-B7","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1471-2105-14-30","article-title":"Seq2Ref: a web server to facilitate functional interpretation","volume":"14","author":"Li","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023012810465063000_btt451-B8","doi-asserted-by":"crossref","first-page":"e1000605","DOI":"10.1371\/journal.pcbi.1000605","article-title":"Annotation error in public databases: misannotation of molecular function in enzyme superfamilies","volume":"5","author":"Schnoes","year":"2009","journal-title":"PLoS Comput. 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