{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T21:12:59Z","timestamp":1779311579428,"version":"3.51.4"},"reference-count":28,"publisher":"World Scientific Pub Co Pte Lt","issue":"03","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2005,6]]},"abstract":"<jats:p> For the identification of novel proteins using MS\/MS, de novo sequencing software computes one or several possible amino acid sequences (called sequence tags) for each MS\/MS spectrum. Those tags are then used to match, accounting amino acid mutations, the sequences in a protein database. If the de novo sequencing gives correct tags, the homologs of the proteins can be identified by this approach and software such as MS-BLAST is available for the matching. However, de novo sequencing very often gives only partially correct tags. The most common error is that a segment of amino acids is replaced by another segment with approximately the same masses. We developed a new efficient algorithm to match sequence tags with errors to database sequences for the purpose of protein and peptide identification. A software package, SPIDER, was developed and made available on Internet for free public use. This paper describes the algorithms and features of the SPIDER software. <\/jats:p>","DOI":"10.1142\/s0219720005001247","type":"journal-article","created":{"date-parts":[[2005,7,19]],"date-time":"2005-07-19T12:06:59Z","timestamp":1121774819000},"page":"697-716","source":"Crossref","is-referenced-by-count":192,"title":["SPIDER: SOFTWARE FOR PROTEIN IDENTIFICATION FROM SEQUENCE TAGS WITH <i>DE NOVO<\/i> SEQUENCING ERROR"],"prefix":"10.1142","volume":"03","author":[{"given":"YONGHUA","family":"HAN","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"BIN","family":"MA","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"KAIZHONG","family":"ZHANG","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2011,11,21]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1038\/nature01511"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1002\/bms.1200190607"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1089\/10665270152530872"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1089\/106652799318300"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1016\/1044-0305(94)80016-2"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0231(19981215)12:23<1867::AID-RCM407>3.0.CO;2-S"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.89.22.10915"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1016\/1044-0305(92)87060-C"},{"key":"rf13","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M008342200"},{"key":"rf14","doi-asserted-by":"publisher","DOI":"10.1089\/106652703763255633"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.3.440"},{"key":"rf16","doi-asserted-by":"publisher","DOI":"10.1002\/rcm.1196"},{"key":"rf18","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M100004-MCP200"},{"key":"rf19","doi-asserted-by":"publisher","DOI":"10.1021\/ac00096a002"},{"key":"rf20","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.85.8.2444"},{"key":"rf21","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/15.9.729"},{"key":"rf22","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2"},{"key":"rf23","first-page":"777","volume":"6","author":"Pevzner P. 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