Reannotation of Shewanella oneidensis genome

OMICS. Summer 2003;7(2):171-5. doi: 10.1089/153623103322246566.

Abstract

As more and more complete bacterial genome sequences become available, the genome annotation of previously sequenced genomes may become quickly outdated. This is primarily due to the discovery and functional characterization of new genes. We have reannotated the recently published genome of Shewanella oneidensis with the following results: 51 new genes have been identified, and functional annotation has been added to the 97 genes, including 15 new and 82 existing ones with previously unassigned function. The identification of new genes was achieved by predicting the protein coding regions using the HMM-based program GeneMark.hmm. Subsequent comparison of the predicted gene products to the non-redundant protein database using BLAST and the COG (Clusters of Orthologous Groups) database using COGNITOR provided for the functional annotation.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / physiology
  • Computational Biology / methods
  • Genes, Bacterial / genetics
  • Genome, Bacterial*
  • Genomics
  • Molecular Sequence Data
  • Open Reading Frames / genetics
  • Sequence Alignment / methods
  • Shewanella / genetics*
  • Software

Substances

  • Bacterial Proteins

Associated data

  • RefSeq/NC_004347