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AuthorRachid, Maan Haj
AuthorMalluhi, Qutaibah
Available date2016-11-14T10:52:16Z
Publication Date2015
Publication NameBioMed Research International
Identifierhttp://dx.doi.org/10.1155/2015/905261
CitationHaj Rachid M, Malluhi Q. A Practical and Scalable Tool to Find Overlaps between Sequences. BioMed Research International. 2015;2015:905261.
ISSN2314-6133
URIhttp://hdl.handle.net/10576/5001
AbstractThe evolution of the next generation sequencing technology increases the demand for efficient solutions, in terms of space and time, for several bioinformatics problems. This paper presents a practical and easy-to-implement solution for one of these problems, namely, the all-pairs suffix-prefix problem, using a compact prefix tree. The paper demonstrates an efficient construction of this time-efficient and space-economical tree data structure. The paper presents techniques for parallel implementations of the proposed solution. Experimental evaluation indicates superior results in terms of space and time over existing solutions. Results also show that the proposed technique is highly scalable in a parallel execution environment.
SponsorNPRP Grant no. 4-1454-1-233 from the Qatar National Research Fund (a member of Qatar Foundation).
Languageen
PublisherHindawi
SubjectAlgorithms
Computational Biology/methods
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA/methods
TitleA Practical and Scalable Tool to Find Overlaps between Sequences
TypeArticle
Volume Number2015
ESSN2314-6141
dc.accessType Open Access


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