Hardness of Optimal Spaced Seed Design

Abstract. Speeding up approximate pattern matching is a line of research in stringology since the 80’s. Practically fast approaches belong to the class of filtration algorithms, in which text regions dissimilar to the pattern are excluded (filtered out) in a first step, and remaining regions are compared to the pattern by dynamic programming in a second step. Among the necessary conditions used to test similarity between the regions and the pattern, many require a minimum number of common substrings between them. When only substitutions are taken into account for measuring dissimilarity, it was shown recently that counting spaced subwords instead of substrings improve the filtration efficiency. However, a preprocessing step is required to design one or more patterns, called gapped seeds, for the subwords, depending on the search parameters. The seed design problems proposed up to now differ by the way the similarities to detect are given: either a set of similarities is given in...

• Type: Conference
• Year: 2005
• Where: CPM
• Authors: François Nicolas, Eric Rivals
• Keywords: Approximate Pattern Matching, Combinatorics, CPM 2005, Region Specific, Seed Design Problem