NDLI: Pairwise Sequence Alignment Method for Distributed Shared Memory Systems

Content Provider	IEEE Xplore Digital Library
Author	Montanola, A. Roig, C. Hernandez, P.
Copyright Year	2013
Description	Author affiliation: Comput. Archit. & Oper. Syst. Dept., Univ. Autonoma de Barcelona, Cerdanyola del Valles, Spain (Hernandez, P.) \|\| Comput. Sci. Dept., Univ. de Lleida, Lleida, Spain (Montanola, A.; Roig, C.)
Abstract	One of the initial key steps of the multiple sequence alignment problem is the pairwise alignment of all pairs of genomic sequences involved. With the increased requirements to align several thousand sequences, it is necessary to find efficient new ways to align as many pairs of sequences as possible. Traditional sequential algorithms are limited by their memory and processing capabilities while parallel implementations running over clusters are able to process considerably more sequences. Nowadays, computer systems are capable of running several processing threads using a shared memory model, which allows us to combine it with distributed memory model. This paper presents a parallel pairwise aligner based on Smith-Waterman capable of processing large numbers of sequences with a small memory footprint. Our implementation is based on the use of a message-passing library such as MPI combined with a threading library, such as pthreads. Our experimentation shows the gain in efficiency for processing different numbers of sequences with different numbers of threads.
Starting Page	432
Ending Page	436
File Size	657517
Page Count	5
File Format	PDF
ISBN	9781467353212
ISSN	10666192
e-ISBN	9781467353212
e-ISBN	9780769549392
DOI	10.1109/PDP.2013.69
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2013-02-27
Publisher Place	UK
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Message systems Instruction sets Computational modeling Libraries Clustering algorithms Bioinformatics Amino acids multi-core sequence alignment shared memory distributed computing
Content Type	Text
Resource Type	Article

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