Paper Info
Title
Fast Structured Motif Search in DNA Sequences
Abstract
We study the problem of structured motif search in DNA sequences. This is a fundamental task in bioinformatics which contributes to better understanding of genome characteristics and properties. We propose an efficient algorithm for Exact Match, Overlapping Structured motif search (EMOS), which uses a suffix tree index we proposed earlier and runs on a typical desktop computer. We have conducted numerous experiments to evaluate EMOS and compared its performance with the best known solution, SMOTIF1 [1]. While in some cases the search time of EMOS is comparable to SMOTIF1, it is on average 5 to 6 times faster.
Year
DOI
Venue
2008
10.1007/978-3-540-70600-7_5
BIOINFORMATICS RESEARCH AND DEVELOPMENT, PROCEEDINGS
Keywords
Field
DocType
DNA sequences,structured motif,suffix tree,performance
Genome,Computer science,Algorithm,Motif (music),Theoretical computer science,DNA sequencing,Suffix tree,Bioinformatics
Conference
Volume
ISSN
Citations 
13
1865-0929
2
PageRank 
References 
Authors
0.38
14
2
Name
Order
Citations
PageRank
Mihail Halachev181.51
Nematollaah Shiri228028.31