{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,2]],"date-time":"2022-04-02T17:25:52Z","timestamp":1648920352402},"reference-count":22,"publisher":"World Scientific Pub Co Pte Lt","issue":"03","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Found. Comput. Sci."],"published-print":{"date-parts":[[2005,6]]},"abstract":"<jats:p> In Biochemistry, tandem mass spectrometry (MS\/MS) is the most common method for peptide and protein identifications. One computational method to get a peptide sequence from the MS\/MS data is called de novo sequencing, which is becoming more and more important in this area. However De novo sequencing usually can only confidently determine partial sequences, while the undetermined parts are represented by \"mass gaps\". We call such a partially determined sequence a gapped sequence tag. When a gapped sequence tag is searched in a database for protein identification, the determined parts should match the database sequence exactly, while each mass gap should match a substring of amino acids whose masses add up to the value of the mass gap. In such a case, the standard string matching algorithm does not work any more. In this paper, we present a new efficient algorithm to find the matches of gapped sequence tags in a protein database. <\/jats:p>","DOI":"10.1142\/s012905410500311x","type":"journal-article","created":{"date-parts":[[2005,7,5]],"date-time":"2005-07-05T10:52:13Z","timestamp":1120560733000},"page":"487-497","source":"Crossref","is-referenced-by-count":0,"title":["AN AUTOMATA APPROACH TO MATCH GAPPED SEQUENCE TAGS AGAINST PROTEIN DATABASE"],"prefix":"10.1142","volume":"16","author":[{"given":"YONGHUA","family":"HAN","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada"}]},{"given":"BIN","family":"MA","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada"}]},{"given":"KAIZHONG","family":"ZHANG","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada"}]}],"member":"219","published-online":{"date-parts":[[2011,11,20]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1038\/nature01511"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.4.634"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1145\/360825.360855"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1002\/bms.1200190607"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-4-66"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1089\/10665270152530872"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1089\/106652799318300"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1016\/1044-0305(94)80016-2"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0231(19981215)12:23<1867::AID-RCM407>3.0.CO;2-S"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1016\/1044-0305(92)87060-C"},{"key":"rf13","doi-asserted-by":"publisher","DOI":"10.1002\/rcm.1196"},{"key":"rf14","first-page":"266","author":"Ma B.","journal-title":"CPM'03"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2"},{"key":"rf16","first-page":"777","volume":"6","author":"Pevzner P. 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