%0 Journal Article %T Commentz-Walter: Any Better than Aho-Corasick for Peptide Identification? %A S.M. Vidanagamachchi %A S.D. Dewasurendra %A R.G. Ragel %J International Journal of Research In Computer Science %D 2012 %I White Globe Publications %X An algorithm for locating all occurrences of a finite number of keywords in an arbitrary string, also known as multiple strings matching, is commonly required in information retrieval (such as sequence analysis, evolutionary biological studies, gene/protein identification and network intrusion detection) and text editing applications. Although Aho-Corasick was one of the commonly used exact multiple strings matching algorithm, Commentz-Walter has been introduced as a better alternative in the recent past. Comments-Walter algorithm combines ideas from both Aho-Corasick and Boyer Moore. Large scale rapid and accurate peptide identification is critical in computational proteomics. In this paper, we have critically analyzed the time complexity of Aho-Corasick and Commentz-Walter for their suitability in large scale peptide identification. According to the results we obtained for our dataset, we conclude that Aho-Corasick is performing better than Commentz-Walter as opposed to the common beliefs. %K aho-corasick %K commentz-walter %K peptide identification %U http://www.ijorcs.org/uploads/archive/Vol2-Issue-06-04-commentz-walter-any-better-than-aho-corasick-for-peptide-identification.pdf