Assembling networks of microbial genomes using linear programming.

ABSTRACT:

Background

Microbial genomes exhibit complex sets of genetic affinities due to lateral genetic transfer. Assessing the relative contributions of parent-to-offspring inheritance and gene sharing is a vital step in understanding the evolutionary origins and modern-day function of an organism, but recovering and showing these relationships is a challenging problem.

Results

We have developed a new approach that uses linear programming to find between-genome relationships, by treating tables of genetic affinities (here, represented by transformed BLAST e-values) as an optimization problem. Validation trials on simulated data demonstrate the effectiveness of the approach in recovering and representing vertical and lateral relationships among genomes. Application of the technique t

SUBMITTER: Holloway C 

PROVIDER: S-EPMC3224671 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature