MISHIMA--a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data.

ABSTRACT:

Background

Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods. Conventional multiple alignment methods are based on pairwise alignment and/or progressive alignment techniques. These approaches have performance problems when the number of sequences is large and when dealing with genome scale sequences.

Results

We present a new method of multiple sequence alignment, called MISHIMA (Method for Inferring Sequence History In terms of Multiple Alignment), that does not depend on pairwise sequence comparison. A new algorithm is used to quickly find rare oligonucleotide sequences shared by all sequences. Divid

SUBMITTER: Kryukov K 

PROVIDER: S-EPMC2848238 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature