Multiple genome alignment for identifying the core structure among moderately related microbial genomes.

ABSTRACT:

Background

Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders.

Results

The method was applied to genome compariso

SUBMITTER: Uchiyama I 

PROVIDER: S-EPMC2615449 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature