[maker-devel] Functional annotation options

[Marc Höppner]

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?

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. 

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