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Browse Conference Publications > Cluster Computing, 2006 IEEE ... Help

Z-align: An Exact and Parallel Strategy for Local Biological Sequence Alignment in User-Restricted Memory Space

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2 Author(s)
Batista, R.B. ; Dept. of Comput. Sci., Brasilia Univ. ; Magalhaes Alves de Melo, Alba Cristina

The algorithm proposed by Smith-Waterman is an exact method that obtains optimal local alignments in quadratic space and time. For long sequences, quadratic complexity makes the use of this algorithm impractical. In this scenario, parallel computing is a very attractive alternative. In this paper, we propose and evaluate z-align, a parallel exact strategy based on the divergence concept to locally align long biological sequences using an affine gap function. Z-align runs in limited memory space, where the amount of memory used can be defined by the user. The results collected in a cluster with 16 processors presented very good speedups for long real DNA sequences. By comparing the results obtained with z-align and BLAST, it is clear that z-align is able to produce longer and more significant alignments

Published in:
Cluster Computing, 2006 IEEE International Conference on

Date of Conference: 25-28 Sept. 2006

Page(s):
1 - 10
ISSN :
1552-5244
E-ISBN :
1-4244-0328-6
Print ISBN:
1-4244-0327-8
INSPEC Accession Number:
9464858
Conference Location :
Barcelona
Digital Object Identifier :
10.1109/CLUSTR.2006.311858
Product Type:
Conference Publications

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