{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T22:15:03Z","timestamp":1759961703529},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,4,1]]},"abstract":"Abstract<\/jats:title>\n Summary: Low-complexity, repetitive protein sequences with a limited amino acid palette are abundant in nature, and many of them play an important role in the structure and function of certain types of proteins. However, such repetitive sequences often do not have rigidly defined motifs. Consequently, the identification of these low-complexity repetitive elements has proven challenging for existing pattern-matching algorithms. Here we introduce a new web-tool SubSeqer (http:\/\/compsysbio.org\/subseqer\/) which uses graphical visualization methods borrowed from protein interaction studies to identify and characterize repetitive elements in low-complexity sequences. Given their abundance, we suggest that SubSeqer represents a valuable resource for the study of typically neglected low-complexity sequences.<\/jats:p>\n Contact: \u00a0jparkin@sickkids.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn073","type":"journal-article","created":{"date-parts":[[2008,2,28]],"date-time":"2008-02-28T01:14:32Z","timestamp":1204161272000},"page":"1016-1017","source":"Crossref","is-referenced-by-count":2,"title":["SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences"],"prefix":"10.1093","volume":"24","author":[{"given":"David","family":"He","sequence":"first","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics and 3Department of Biochemistry, University of Toronto, Toronto, Canada"},{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics and 3Department of Biochemistry, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Parkinson","sequence":"additional","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics and 3Department of Biochemistry, University of Toronto, Toronto, Canada"},{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics and 3Department of Biochemistry, University of Toronto, Toronto, Canada"},{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics and 3Department of Biochemistry, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,2,26]]},"reference":[{"key":"2023020209533387300_B1","doi-asserted-by":"crossref","first-page":"i9","DOI":"10.1093\/bioinformatics\/bti1051","article-title":"Conservative extraction of over-represented extensible motifs","volume":"21","author":"Apostolico","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020209533387300_B2","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers","volume":"2","author":"Bailey","year":"1994","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol"},{"key":"2023020209533387300_B3","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"key":"2023020209533387300_B4","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1016\/j.matbio.2007.05.005","article-title":"Comparative genomics of elastin: sequence analysis of a highly repetitive protein","volume":"26","author":"He","year":"2007","journal-title":"Matrix Biol"},{"key":"2023020209533387300_B5","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1093\/bioinformatics\/14.1.55","article-title":"Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm","volume":"14","author":"Rigoutsos","year":"1998","journal-title":"Bioinformatics"},{"key":"2023020209533387300_B6","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1098\/rstb.2001.1031","article-title":"Comparative structures and properties of elastic proteins","volume":"357","author":"Tatham","year":"2002","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci"},{"key":"2023020209533387300_B7","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/0097-8485(94)85023-2","article-title":"Non-globular domains in protein sequences: automated segmentation using complexity measures","volume":"18","author":"Wootton","year":"1994","journal-title":"Comput. Chem"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/7\/1016\/49048813\/bioinformatics_24_7_1016.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/7\/1016\/49048813\/bioinformatics_24_7_1016.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T09:59:13Z","timestamp":1675331953000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/7\/1016\/298292"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,2,26]]},"references-count":7,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2008,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn073","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,4,1]]},"published":{"date-parts":[[2008,2,26]]}}}