[Inparanoid] local run inparanoid_4.1 found only 5779 mouse protein are orthologs of human
Pengcheng Yang
yangpc at biols.ac.cn
Sun Aug 19 12:21:13 CEST 2018
Dear colleagues,
I have run Inparanoid_4.1 between my studied organism and human. As
comparison, I run the same program between mouse and human. These two
runs used the same human protein data set and same program, but with
different input species A. But the identified ortholog in mouse was only
5779, it is very strange. So I run the same program with Rat and human
as input species A and B. The Rat displayed 16979 orthologs of human,
which is reasonable.
1. I have checked the blast results and found there areĀ 21745
(mouse.pep-human.fa), 21733 (human.fa-mouse.pep), and 18017
(mouse.pep-mouse.pep) unique mouse protein IDs. These results suggested
that the blast step is ok.
2. I checked the message output from inparanoid.pl, and found the
warning message from mouse are 27849 lines, in contrast, only 439 lines
from rat. It seems this problem was originated from the "ortholog
detection" step.
I have rerun the program several times, but with the same results.
Because I used the exactly same program with same parameters, I don't
know how to debug this problem. Could anyone help me out?
Best,
Pengcheng Yang
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