MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution | Zendy

Peter D. Keightley | Zendy; Toby Johnson | Zendy

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MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution

Author(s) -

Peter D. Keightley,

Toby Johnson

Publication year - 2004

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.1571904

Subject(s) - indel , biology , multiple sequence alignment , phylogenetic tree , sequence (biology) , genetics , parameterized complexity , noncoding dna , computational biology , alignment free sequence analysis , dna sequencing , sequence alignment , range (aeronautics) , dna , algorithm , evolutionary biology , gene , intron , mathematics , peptide sequence , composite material , materials science , genotype , single nucleotide polymorphism

A method is described for performing global alignment of noncoding DNA sequences based on an evolutionary model parameterized by the frequency distribution of lengths of insertion/deletion events (indels) and their rate relative to nucleotide substitutions. A stochastic hill-climbing algorithm is used to search for the most probable alignment between a pair of sequences or three sequences of known phylogenetic relationship. The performance of the procedure, parameterized according to the empirical distribution of indel lengths in noncoding DNA of Drosophila species, is investigated by simulation. We show that there is excellent agreement between true and estimated alignments over a wide range of sequence divergences, and that the method outperforms other available alignment methods.

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