Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes.

ABSTRACT:

Background

Lineage-specific, or taxonomically restricted genes (TRGs), especially those that are species and strain-specific, are of special interest because they are expected to play a role in defining exclusive ecological adaptations to particular niches. Despite this, they are relatively poorly studied and little understood, in large part because many are still orphans or only have homologues in very closely related isolates. This lack of homology confounds attempts to establish the likelihood that a hypothetical gene is expressed and, if so, to determine the putative function of the protein.

Methodology/principal findings

We have developed "QIPP" ("Quality Index for Predicted Proteins"), an index that scores the "quality" of a protein based on non-homology-based criteria

SUBMITTER: Wilson GA 

PROVIDER: S-EPMC1824705 | biostudies-literature | 2007 Mar

REPOSITORIES: biostudies-literature