Virginia Bioinformatics Institute (VBI) Genome Annotation Series
Plant-Associated Microbe Gene Ontology (PAMGO) Training Workshop - August 8-10, 2007
Oomycete Bioinformatics Resources Training Workshop - August 8-10, 2007

Some useful links for the workshop

• VBI
• DOE JGI - Psojae
• DOE JGI - Pramorum
• BROAD INSTITUTE : P.infestans
• NCGR
• PhIGS Synteny Browser

Other Resources

• Cogeme
• Community Web Site
• Phytophthora Moelcular Identification Database
• TIGR Comprehensive Phytopathogens Genomics Resource
• PAMGO
• JGI Tutorial

Hyaloperonospora parasitica Genome Annotation

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

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