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...

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Vydáno v:Journal of bioinformatics and computational biology Ročník 10; číslo 4; s. 1250002
Hlavní autoři: Kimura, Kouichi, Koike, Asako, Nakai, Kenta
Médium: Journal Article
Jazyk:angličtina
Vydáno: Singapore 01.08.2012
Témata:
Algorithms
Base Sequence
Computational Biology
DNA - chemistry
Genome
Sequence Alignment
Sequence Analysis, DNA
ISSN:1757-6334, 1757-6334
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Shrnutí: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.
Bibliografie:ObjectType-Article-1
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ISSN:1757-6334
1757-6334
DOI:10.1142/S0219720012500023