[maker-devel] Functional annotation options

[Mikael Brandström Durling]

26 feb 2014 kl. 09:26 skrev Marc Höppner <marc.hoeppner at imbim.uu.se>:

> Dear List,
> 
> I have finished a gene build now, and I would like to go over to functional annotation. I understand that maker includes a few script to facilitate such analyses. However, I have a few questions about this:
> 
> 1) iprscan
> It seems maker includes a MPI wrapper for InterProscan, but requests ‘iprscan’ to be in $PATH. The latest versions of Interproscan I have worked with are java applications and eventho I put their location in $PATH, mpi_iprscan seems to want something else? But what?

I don’t believe it works with interproscan5. What I usually do is to split the maker protein file into chunks, and then run these chunks as separate jobs on our cluster, then finally merge the results. The TSV file form iprscan5 can be input into the maker tool ipr_update_gff. I have not tried the iprscan2gff3, as I haven’t figured how to get an iprscan4 raw file from iprscan5.


> 2) maker_functional_gff
> This script seems to be very useful, but the description suggests that it requires WuBlast tabular output ‘2', which I think looks quite different from the ncbi blast tabular output. Since Wublast is not really available anymore (except this very old, frozen binary bundle), I was wondering how to address this issue. 

It works fine with ncbiblast+ and the blastp command with -outfmt 6. 

cheers,
Mikael

Ps. Your welcome to visit me at SLU if you would like to discuss experiences of genome annotations.


> 
> 3) maker_functional
> This just throws an error about a missing Job ID, so no clue what this would be used for.
> 
> I guess what I am after is some suggestion as to how use the scripts included with Maker to achieve a reasonable functional annotation. 
> 
> With kind regards,
> 
> Marc Hoeppner
> 
> Marc P. Hoeppner, PhD
> Team Leader
> BILS Genome Annotation Platform
> Department for Medical Biochemistry and Microbiology
> Uppsala University, Sweden
> marc.hoeppner at imbim.uu.se
> 
> 
> 
> 
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