Paper Abstract and Keywords |
Presentation |
2005-09-15 14:35
A Polynomial Space Polynomial Delay Algorithm for Enumerating Maximal Motifs in a Sequence Hiroki Arimura (Hokkaido Univ.), Takeaki Uno (NII) |
Abstract |
(in Japanese) |
(See Japanese page) |
(in English) |
In this paper, we consider the problem of finding all maximal motifs in an input string for the class of repeated motifs with wild cards, which has various applications in bioinformatics, sequence mining, and data compression. Since its proposal, its output-sensitive enumeration has been studied, but no algorithms achieved polynomial space and polynomial delay so far. For the problem, we present a polynomial space polynomial delay algorithm for the maximal motif enumeration problem for the repeated motifs with wild cards. We also show exponential lower bound and succinctness results on the number of maximal motifs, which indicate the limit of a straightforward approach. |
Keyword |
(in Japanese) |
(See Japanese page) |
(in English) |
Enumeration algorithms / Maximal motif discovery / Basis of tiling motifs / Bioinformatics / / / / |
Reference Info. |
IEICE Tech. Rep., vol. 105, no. 273, COMP2005-32, pp. 31-38, Sept. 2005. |
Paper # |
COMP2005-32 |
Date of Issue |
2005-09-08 (COMP) |
ISSN |
Print edition: ISSN 0913-5685 |
Download PDF |
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Conference Information |
Committee |
COMP |
Conference Date |
2005-09-15 - 2005-09-15 |
Place (in Japanese) |
(See Japanese page) |
Place (in English) |
Osaka Univ., Toyonaka Campus |
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(See Japanese page) |
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Paper Information |
Registration To |
COMP |
Conference Code |
2005-09-COMP |
Language |
English (Japanese title is available) |
Title (in Japanese) |
(See Japanese page) |
Sub Title (in Japanese) |
(See Japanese page) |
Title (in English) |
A Polynomial Space Polynomial Delay Algorithm for Enumerating Maximal Motifs in a Sequence |
Sub Title (in English) |
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Keyword(1) |
Enumeration algorithms |
Keyword(2) |
Maximal motif discovery |
Keyword(3) |
Basis of tiling motifs |
Keyword(4) |
Bioinformatics |
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1st Author's Name |
Hiroki Arimura |
1st Author's Affiliation |
Hokkaido University (Hokkaido Univ.) |
2nd Author's Name |
Takeaki Uno |
2nd Author's Affiliation |
National Institute of Informatics (NII) |
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Speaker |
Author-1 |
Date Time |
2005-09-15 14:35:00 |
Presentation Time |
35 minutes |
Registration for |
COMP |
Paper # |
COMP2005-32 |
Volume (vol) |
vol.105 |
Number (no) |
no.273 |
Page |
pp.31-38 |
#Pages |
8 |
Date of Issue |
2005-09-08 (COMP) |
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