[maker-devel] InterProScan protein domain & AED physical evidence filtering

[Allison Fuiten]

Hello MAKER google group,



For the final round of a MAKER annotation for a de novo plant genome
assembly, I ran MAKER twice: once with keep_preds=0 which annotated 20,284
genes and once with keep_preds=1 which annotated 34,055 genes.



I ran the 34,055 genes (the keep_preds=1 set) through InterProScan to
search the MAKER predictions for protein domain content and added this
IPRScan output into the MAKER gff file with the ipr_update_gff accessory
script.



The game plan is to go through the 34,055 genes and remove any gene model
that doesn’t have either protein domain content or physical evidence. I am
counting genes that have an AED=1 as the genes that don’t have physical
evidence.



I have two questions:


1. I count 11,762 genes that have AED=1.0 in the keep_preds=1 annotation
set, which leaves me with 22,293 genes that I’m assuming have some physical
evidence (34,055-11,762=22,293).  But when I ran MAKER with keep_preds=0
originally, I only count 20,284 genes. What are the extra ~2,000 genes that
are being annotated in the keep_preds=1 run that have and AED score of less
than 1.0, but are not being annotated in the keep_preds=0 run?



2. My second question is if there is an accessory script available that
will remove genes that lack either the IPRScan protein domains or physical
evidence (AED < 1)? This type of gene removal was mentioned in a previous
post from 2012 (https://groups.google.com/forum/#!searchin/maker-devel/
sorry$20there$27s$20not$20a$20script$20prepackaged$20with$
20MAKER$20for$20that$20yet.%7Csort:relevance/maker-devel/
VaoXWlGHOjs/EElr_otrK8QJ) and I was just wondering if since then someone
wrote a script that will do this for me.


If anyone could offer me any feedback, that would be greatly appreciated!


Thank you,


Allison
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