Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes.

ABSTRACT:

Background

With the number of available genome sequences increasing rapidly, the magnitude of sequence data required for multiple-genome analyses is a challenging problem. When large-scale rearrangements break the collinearity of gene orders among genomes, genome comparison algorithms must first identify sets of short well-conserved sequences present in each genome, termed anchors. Previously, anchor identification among multiple genomes has been achieved using pairwise alignment tools like BLASTZ through progressive alignment tools like TBA, but the computational requirements for sequence comparisons of multiple genomes quickly becomes a limiting factor as the number and scale of genomes grows.

Methodology/principal findings

Our algorithm, named Murasaki, makes it possible

SUBMITTER: Popendorf K 

PROVIDER: S-EPMC2945767 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature