Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.

ABSTRACT:

Background

The dramatic reduction in the cost of sequencing has allowed many researchers to join in the effort of sequencing and annotating prokaryotic genomes. Annotation methods vary considerably and may fail to identify some genes. Here we draw attention to a large number of likely genes missing from annotations using common tools such as Glimmer and BLAST.

Results

By analyzing 1,474 prokaryotic genome annotations in GenBank, we identify 13,602 likely missed genes that are homologs to non-hypothetical proteins, and 11,792 likely missed genes that are homologs only to hypothetical proteins, yet have supporting evidence of their protein-coding nature from COMBREX, a newly created gene function database. We also estimate the likelihood that each potential missing gene found

SUBMITTER: Wood DE 

PROVIDER: S-EPMC3534567 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature