The MicrobesOnline genome database contains over 1000 prokaryotic genomes.

All genomes are analyzed through the VIMSS genome pipeline. We use publicly available sequence analysis tools and databases to search for homologs (NCBI BLAST, UCSC Blat, SwissProt, COG) and protein domains (FastHMM, InterPro), to assign gene ontologies (Gene Ontology Consortium) and EC numbers and to map the metabolic pathways (KEGG). We then link the orthology relationships between genes, and predict operon structures and regulon networks.

Most genome data is downloaded from RefSeq. When an incomplete genome is directly downloaded from a sequencing center, we predict protein coding genes using CRITICA and Glimmer3, tRNA genes using tRNAscan, and other RNA genes by BLASTn. For all genomes, we search for CRISPR regions using PILER-CR and CRT.

All of the information in the VIMSS genome database is freely available on our website.

Currently we use these versions of external databases:

• RefSeq: Release 41, May 2010 (complete microbial genomes plus selected WGS genomes)
• COG: CDD 2.21 April 2010 (from NCBI CDD)
• PDB: June 2010
• KEGG: April 2009
• UniProt/SwissProt: UniProt 15.0, SwissProt 57.0, March 2009
• InterPro: release 4.6, February 2010
  • All except TIGRFam: data 26.0, March 2010.
  • TIGRFam: 9.0. See our FastHMM tool, written by the MicrobesOnline team, for more information.
• Gene Ontology: 200711

We update our analyses with the latest release of each database every six-twelve months.

last updated July 2010

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