How does VFDB work?

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4.6 years ago

baohiep2013 ▴ 10

Hi everyone,

I'm creating a pipeline for Helicobacter Pylori that needs report from VFDB. Currently I'm sending FASTA files to VFDB and getting reports back. Apparently, it's pretty slow, so I'm trying to implement VFDB in my pipeline.

The problem is that VFDB is not open-sourced. Does anyone know how it works? It seems to use OrthoMCL, but I don't know why...

Please help me!

vfdb • 1.4k views

ADD COMMENT • link 4.6 years ago by baohiep2013 ▴ 10

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VFDB, the Virulence Factors Database? The download page can help http://www.mgc.ac.cn/VFs/download.htm

ADD REPLY • link 4.6 years ago by gb ★ 2.2k

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I will add that you can have a global look of their analysis pipeline in their paper: https://www.ncbi.nlm.nih.gov/pubmed/30395255

Maybe with that information and the data you can get from their download page you can get somewhere. You can for instance, run a simple blast for the VF sequences for your organism, the results won't be as good as their whole pipeline but maybe it can be enough. The thing I really like about VFDB is that you can just search the VF and get functional/structural informations. I mostly use it to look in which mechanism a VF I found is involved.

ADD REPLY • link 4.6 years ago by Sus ▴ 40

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