Efficient q-gram filters for finding all epsilon-matches over a given length

J Comput Biol. 2006 Mar;13(2):296-308. doi: 10.1089/cmb.2006.13.296.


Fast and exact comparison of large genomic sequences remains a challenging task in biosequence analysis. We consider the problem of finding all epsilon-matches between two sequences, i.e., all local alignments over a given length with an error rate of at most epsilon. 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.

Publication types

  • Comparative Study

MeSH terms

  • Algorithms*
  • Computational Biology*
  • Databases, Nucleic Acid
  • Genome*
  • Sensitivity and Specificity
  • Sequence Alignment / statistics & numerical data*