ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.

ABSTRACT:

Background

Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms.

Methodology/principal findings

We describe a new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss (flux). We demonstrate that the new method can accurately align regions conserved in some, but not all, of the genomes, an important case not handled by our previous work. The method uses a novel alignment objective score called a sum-of-pairs breakpoint score, which facilitates accurate detection of rearrangement breakpoints when genomes have unequal gene

SUBMITTER: Darling AE 

PROVIDER: S-EPMC2892488 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature