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RISOTTO: Fast extraction of motifs with mismatches (2006)
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| Venue: | PROCEEDINGS OF THE 7TH LATIN AMERICAN THEORETICAL INFORMATICS SYMPOSIUM, 3887 OF LNCS:757–768 |
| Citations: | 16 - 5 self |
BibTeX
@INPROCEEDINGS{Pisanti06risotto:fast,
author = {Nadia Pisanti and Alexandra M. Carvalho and Laurent Marsan and Marie-france Sagot},
title = {RISOTTO: Fast extraction of motifs with mismatches},
booktitle = {PROCEEDINGS OF THE 7TH LATIN AMERICAN THEORETICAL INFORMATICS SYMPOSIUM, 3887 OF LNCS:757–768},
year = {2006},
pages = {757--768},
publisher = {Springer-Verlag}
}
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Abstract
We present in this paper an exact algorithm for motif extraction. Efficiency is achieved by means of an improvement in the algorithm and data structures that applies to the whole class of motif inference algorithms based on suffix trees. An average case complexity analysis shows a gain over the best known exact algorithm for motif extraction, when applied to extract long motifs. A full implementation was developed and made available online. Experimental results show that the proposed algorithm is more than two times faster than the best known exact algorithm for motif extraction, confirming in this way the theoretical results obtained.
