A bit-parallel dynamic programming algorithm suitable for DNA sequence alignment

Myers' elegant and powerful bit-parallel dynamic programming algorithm for approximate string matching has a restriction that the query length should be within the word size of the computer, typically 64. We propose a modification of Myers' algorithm, in which the modification has a restri...

Full description

Saved in:
Bibliographic Details
Published in:Journal of bioinformatics and computational biology Vol. 10; no. 4; p. 1250002
Main Authors: Kimura, Kouichi, Koike, Asako, Nakai, Kenta
Format: Journal Article
Language:English
Published: Singapore 01.08.2012
Subjects:
Algorithms
Base Sequence
Computational Biology
DNA - chemistry
Genome
Sequence Alignment
Sequence Analysis, DNA
ISSN:1757-6334, 1757-6334
Online Access:Get more information
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Myers' elegant and powerful bit-parallel dynamic programming algorithm for approximate string matching has a restriction that the query length should be within the word size of the computer, typically 64. We propose a modification of Myers' algorithm, in which the modification has a restriction not on the query length but on the maximum number of mismatches (substitutions, insertions, or deletions), which should be less than half of the word size. The time complexity is O(m log |Σ|), where m is the query length and |Σ| is the size of the alphabet Σ. Thus, it is particularly suited for sequences on a small alphabet such as DNA sequences. In particular, it is useful in quickly extending a large number of seed alignments against a reference genome for high-throughput short-read data produced by next-generation DNA sequencers.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1757-6334
1757-6334
DOI:10.1142/S0219720012500023