New Bit-Parallel Indel-Distance Algorithm [chapter]

Heikki Hyyrö, Yoan Pinzon, Ayumi Shinohara
2005 Lecture Notes in Computer Science  
The task of approximate string matching is to find all locations at which a pattern string p of length m matches a substring of a text string t of length n with at most k differences. It is common to use Levenshtein distance [5] , which allows the differences to be single-character insertions, deletions, substitutions. Recently, in [3] , the IndelMYE, In-delWM and IndelBYN algorithms where introduced as modified version of the bit-parallel algorithms of Myers [6], Wu&Manber [10] and
more » ... Navarro [1], respectively. These modified versions where made to support the indel distance (only single-character insertions and/or deletions are allowed). In this paper we present an improved version of IndelMYE that makes a better use of the bit-operations and runs 24.5 percent faster in practice. In the end we present a complete set of experimental results to support our findings.
doi:10.1007/11427186_33 fatcat:q2puyzdrljg3bmztlhhbwdcvu4