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Bioinformatics Advance Access published online on February 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti323
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received October 11, 2004
Revised January 13, 2005
Accepted February 9, 2005

Article

Using sequence compression to speedup probabilistic profile matching

Valerio Freschi 1 and Alessandro Bogliolo 1*

1 Information Science and Technology Institute, University of Urbino 61029 Urbino, Italy

* To whom correspondence should be addressed.
Alessandro Bogliolo, E-mail: bogliolo{at}sti.uniurb.it


  Abstract

Motivation: Matching a biological sequence against a probabilistic pattern (or profile) is a common task in computational biology. A probabilistic profile, represented as a scoring matrix, is more suitable than a deterministic pattern to retain the peculiarities of a given segment of a family of biological sequences. Brute-force algorithms take O(NP) to match a sequence of N characters against a profile of length P << N.

Results: In this work, we exploit string compression techniques to speedup brute-force profile matching. We present two algorithms, based on run-length and LZ78 encodings, that reduce computational complexity by the compression factor of the encoding.


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