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, UCSC Blat, 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 28, March 2008
• COG: November 2007 (from NCBI CDD)
• PDB: 20071005
• KEGG: March 2008
• UniProt/SwissProt: UniProt 13.1, SwissProt 55.1, March 2008
• InterPro: release 4.3.1, January 2007
  • BlastProDom, Coils, FPrintScan, ScanRegExp, Seg: data 17.0, March 2008
  • For the HMM-based InterPro searches, we use a new process called FastHMM.
• Gene Ontology: 200711

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

last updated April 7, 2008

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