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Paper Abstract and Keywords
Presentation 2012-09-03 11:25
Compressing de Bruijn Graphs
Alexander Bowe (NII), Taku Onodera (Univ. of Tokyo), Kunihiko Sadakane (NII), Tetsuo Shibuya (Univ. of Tokyo)
Abstract (in Japanese) (See Japanese page) 
(in English) We propose a new succinct de Bruijn graph representation.
If the de Bruijn graph of $k$-mers in a DNA sequence of length $N$ has $m$ edges,
it can be represented in $4m + \order(m)$ bits.
This is much smaller than existing ones.
The numbers of outgoing and incoming edges of a node are computed in constant time, and
the outgoing and incoming edge with given label are found in constant time
and $\Order(k)$ time, respectively.
The data structure is constructed in $\Order(Nk \log m/\log\log m)$
time using no additional space.
Keyword (in Japanese) (See Japanese page) 
(in English) de Bruijn graph / genome assembly / succinct data structures / / / / /  
Reference Info. IEICE Tech. Rep., vol. 112, no. 199, COMP2012-29, pp. 25-32, Sept. 2012.
Paper # COMP2012-29 
Date of Issue 2012-08-27 (COMP) 
ISSN Print edition: ISSN 0913-5685  Online edition: ISSN 2432-6380

Conference Information
Committee COMP  
Conference Date 2012-09-03 - 2012-09-03 
Place (in Japanese) (See Japanese page) 
Place (in English) Hosei University 
Topics (in Japanese) (See Japanese page) 
Topics (in English)  
Paper Information
Registration To COMP 
Conference Code 2012-09-COMP 
Language English (Japanese title is available) 
Title (in Japanese) (See Japanese page) 
Sub Title (in Japanese) (See Japanese page) 
Title (in English) Compressing de Bruijn Graphs 
Sub Title (in English)  
Keyword(1) de Bruijn graph  
Keyword(2) genome assembly  
Keyword(3) succinct data structures  
1st Author's Name Alexander Bowe  
1st Author's Affiliation National Institute of Informatics (NII)
2nd Author's Name Taku Onodera  
2nd Author's Affiliation The University of Tokyo (Univ. of Tokyo)
3rd Author's Name Kunihiko Sadakane  
3rd Author's Affiliation National Institute of Informatics (NII)
4th Author's Name Tetsuo Shibuya  
4th Author's Affiliation The University of Tokyo (Univ. of Tokyo)
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Date Time 2012-09-03 11:25:00 
Presentation Time 35 
Registration for COMP 
Paper # IEICE-COMP2012-29 
Volume (vol) IEICE-112 
Number (no) no.199 
Page pp.25-32 
#Pages IEICE-8 
Date of Issue IEICE-COMP-2012-08-27 

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