Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length

Rasmussen KR, Stoye J, Myers EW. Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length. In: Proc. of RECOMB 2005. LNBI. Vol 3500. SPRINGER-VERLAG BERLIN; 2005: 189-203.Fast and exact comparison of large genomic sequences remains a challenging task in biosequence analysis. We consider the problem of finding all c-matches between two sequences, i.e. all local alignments over a given length with an error rate of at most E. We study this problem theoretically, giving an efficient q-gram filter for solving it. Two applications of the filter are also discussed, in particular genomic sequence assembly and BLAST-like sequence comparison. Our results show that the method is 25 times faster than BLAST, while not being heuristic