The MicrobesOnline genome database contains over 700 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, SwissProt, COG) and protein domains (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, 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 Glimmer, tRNA genes using tRNAscan and other RNA genes by BLASTn.

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 22, March 2007
• COG: April 2007 (from NCBI CDD)
• PDB: 20071005
• KEGG: April 2007
• UniProt/SwissProt: UniProt 10.2, SwissProt 52.2, April 2007
• InterPro: release 4.3.1, January 2007
  • BlastProDom, Coils, FPrintScan, ScanRegExp, Seg: data 15.0, April 2007
  • For the HMM-based InterPro searches, we use a new process called FastHMM.
• Gene Ontology: March 2006

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

last updated November 1, 2007

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