Re-annotation of protein-coding genes in 10 complete genomes of Neisseriaceae family by combining similarity-based and composition-based methods.

ABSTRACT: In this paper, we performed a comprehensive re-annotation of protein-coding genes by a systematic method combining composition- and similarity-based approaches in 10 complete bacterial genomes of the family Neisseriaceae. First, 418 hypothetical genes were predicted as non-coding using the composition-based method and 413 were eliminated from the gene list. Both the scatter plot and cluster of orthologous groups (COG) fraction analyses supported the result. Second, from 20 to 400 hypothetical proteins were assigned with functions in each of the 10 strains based on the homology search. Among newly assigned functions, 397 are so detailed to have definite gene names. Third, 106 genes missed by the original annotations were picked up by an ab initio gene finder combined with similarity alignme

SUBMITTER: Guo FB 

PROVIDER: S-EPMC3686433 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature