Paper Info
Title
Searching for Supermaximal Repeats in Large DNA Sequences
Abstract
We study the problem of finding supermaximal repeats in large DNA sequences. For this, we propose an algorithm called SMR which uses an auxiliary index structure (POL), which is derived from and replaces the suffix tree index ST-FD64 [1]. The results of our numerous experiments using the 24 human chromosomes data indicate that SMR outperforms the solution provided as part of the Vmatch [2] software tool. In searching for supermaximal repeats of size at least 10 bases, SMR is twice faster than Vmatch; for a minimum length of 25 bases, SMR is 7 times faster; and for repeats of length at least 200, SMR is about 9 times faster. We also study the cost of POL in terms of time and space requirements.
Year
DOI
Venue
2008
10.1007/978-3-540-70600-7_7
BIOINFORMATICS RESEARCH AND DEVELOPMENT, PROCEEDINGS
Keywords
Field
DocType
DNA sequences,supermaximal repeats,suffix tree,performance
Software tool,Computer science,Algorithm,Theoretical computer science,DNA sequencing,Suffix tree,Bioinformatics
Conference
Volume
ISSN
Citations 
13
1865-0929
2
PageRank 
References 
Authors
0.37
10
3
Name
Order
Citations
PageRank
Chen Na Lian120.37
Mihail Halachev281.51
Nematollaah Shiri328028.31