VMD Version 4.0

  • Annotations updated.
  • H.arabidopsidis V7.1 assembly available for download. V7.1 assembly is a manually curated assembly of V7.0 with the BAC assemblies.
  • New Blast viewer available

Version 3.0 assembly of Hyaloperonospora parasitica was released on July 11th 2007. Gene calling on this was done using genezilla(formerly TIGRSCAN) and SNAP. There were 12,000 common gene models from these 2 gene calls. The best gene calls were filtered after checking their coding potential using loglikelihood and hexamer frequency. Additionally, Fickett statistics is used to validate the models. The matching as well as non-matching gene calls were analyzed with the following programs:
  • BLASTX
  • INTERPROSCAN
  • SIGNALP
  • TMHMM
  • KEGG PATHWAY ANALYSIS TOOL
  • SIM4

The outputs were parsed and stored in VBI Microbial Database(VMD). VMD is a slightly modified version of GUS. We have modified GUS slightly to fit into our requirement. Click here to find more on our GUS documentation.

Download Gene Models and GFF Files

  • Download final gene models here
  • Download genezilla gene models here
  • Download SNAP gene models here
  • Download genezilla gff file here
  • Download SNAP gff file here
  • Download gene model id - new gene id mapping filehere

    VBI microbial database is featured in Science netwatch section.Click here for details


VBI Microbial Database at VBI hosts data from a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at VBI. The data comes from different sources. The database is a modified version of Genome Unified Schema(GUS). To browse the genome data of varous organisms click on the images on each organism.
Comments/questions:
sutripa@vbi.vt.edu