[maker-devel] Functional annotation options

[Carson Holt]

maker_functional is a script that gets called by another script, not meant
to be called directly by the user.  So ignore that.

Just run iprscan directly it already works pretty well.  The mpi_iprscan
and iprscan_wrap scripts, just give some logging functionality by wrapping
the iprscan call.  In most cases there is not advantage over just running
iprscan directly.

—Carson




On 2/26/14, 2:43 AM, "Mikael Brandström Durling" <mikael.durling at slu.se>
wrote:

>
>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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>
>
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