RT Journal
A1 Keightley, Peter D.
A1 Johnson, Toby
T1 MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution
JF Genome Research 
JO Genome Research 
YR 2004 
FD March 01 
VO 14 
IS 3 
SP 442 
OP 450 
DO 10.1101/gr.1571904 
UL http://genome.cshlp.org/content/14/3/442.abstract 
AB 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.