How to assign genes of bacterial species to orthologous groups built in HelmCop

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yizi yang

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Dec 10, 2012, 3:20:53 AM12/10/12
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Hi, everyone,

Orthologous groups in HelmCop were inferred using OrthoMCL. Genomes of some bacterial species were included in OrthoMCL DB. I would like to know how to assign genes of these bacterial species into orthologous groups in HelmCop. Could anyone offer me any suggestion?

Thanks a lot!

Yizi

John Martin

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Dec 13, 2012, 9:01:32 PM12/13/12
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Yizi,
    No bacterial organisms were included in the OrthoMCL job used to define the orthologous groups in HelmCoP, so I am confused by your question. But if you have your own bacterial gene that you want to search for amongst the HelmCoP proteins, you can use the HelmCoP BLAST page (http://nematode.net/NN3_frontpage.cgi?navbar_selection=search&subnav_selection=helmcop_blast) to search your gene against the organisms in the HelmCoP groups.  If you have a strong hit, you could infer that your bacterial gene might be orthologous to the group in which the HelmCoP protein you hit belongs.

John
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