Introduction

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.

Publications

  1. Efficient q-gram filters for finding all epsilon-matches over a given length.
    Cite this
    Rasmussen KR, Stoye J, Myers EW, 2006-03-01 - Journal of computational biology : a journal of computational molecular cell biology

Credits

  1. Kim R Rasmussen
    Developer

  2. Jens Stoye
    Developer

  3. Eugene W Myers
    Investigator

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Summary
AccessionBT006597
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByEugene W Myers