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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
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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 
Topics (in Japanese) (See Japanese page) 
Topics (in English)  
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)  
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
Date of Issue 2005-09-08 (COMP) 


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