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Sci Rep. 2013;3:1746. doi: 10.1038/srep01746.

FOGSAA: Fast Optimal Global Sequence Alignment Algorithm.

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1
Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India.

Abstract

In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, with any scoring scheme, and with or without affine gap penalty. Compared to NW, FOGSAA achieves a time gain of (70-90)% for highly similar nucleotide sequences (> 80% similarity), and (54-70)% for sequences having (30-80)% similarity. For other sequences, it terminates with an approximate score. For protein sequences, the average time gain is between (25-40)%. Compared to three heuristic global alignment methods, the quality of alignment is improved by about 23%-53%. FOGSAA is, in general, suitable for aligning any two sequences defined over a finite alphabet set, where the quality of the global alignment is of supreme importance.

PMID:
23624407
PMCID:
PMC3638164
DOI:
10.1038/srep01746
[Indexed for MEDLINE]
Free PMC Article
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