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CONTRIBUTORS:
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PROCEEDINGS TITLE:
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YEAR:
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2008
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PUB TYPE:
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Conference Paper in Proceedings
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PAGES:
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n/a -
n/a
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SUBJECT(S):
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multiple sequence alignment; nucleotide sequences; ant colony optimization
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DISCIPLINE:
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Computer Science
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HTTP:
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http://www.ics.uplb.edu.ph/node/272
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LANGUAGE:
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English
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PUB ID:
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103-444-116
(Last edited on
2008/07/18 21:58:49 GMT-6)
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SPONSOR(S):
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ABSTRACT:
This paper presents a novel procedure for aligning multiple sequences using a simplified stigmergic behavior of a colony of ants as a computational model. Also presented are current results of comparing the performance of the model in aligning sequences from a known benchmark sequence database with that of existing methodologies: FASTA for pairwise alignment and Clustal~W for multiple sequence alignment. Comparison of the resulting alignment scores using the objective function defined in this study shows that the simple ant model was able to output a similar quality alignment as FASTA and Clustal~W at a lesser wall clock time but will need an extra optimization step to reduce the extra gaps inserted. Studies on the effect of the optimization step in the quality of the resulting alignment and the runtime of the model are currently underway.
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