This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Running Sift And Polyphen In Mouse And Other Species

Hello,

Can we annotate missense mutations in other species (e.g. mouse) with Sift and Polyphen? If not, what are the equivalent software for mouse?

Thanks
Simon

sift polyphen
• 8,870 views • link
updated by Ram Ram • written by jeansimon32 • jeansimon32

To run Polyphen2 on mouse genes you will have to build the mouse database from scratch. The steps required can be read in the Polyphen2 manual. Download the Polyphen2 binaries and build your mouse database using protein sequences from UniProt. You can then use command line to find out how deleterious is the missense mutation.

• 215 views • link
written by Ashutosh Pandey Ashutosh Pandey

Hi, I saw your post and thought to ask for help.

I am trying to build the mouse database from scratch to use polyphen2 using the manual, but I keep getting the following error:

/Software/polyphen-2.2.2/bin/run_pph.pl mouse.test.input 1>mouse.test.output
DBD::SQLite::db prepare failed: no such table: id2acc at /NGS/Software/polyphen-2.2.2/perl/PPH/Seq.pm line 89, <> line 1.

Not sure why and what is going wrong. Any help will be much appreciated.

Thanks,
Saumya

• 1 views • link
updated by Ram Ram • written by somseeprags • somseeprags

2 answers

You can absolutely run SIFT on any species. In Ensembl, we have SIFT predictions for every possible amino acid change in the genome for human, mouse, rat, dog, chicken and cow, and will be introducing sheep in our next release in December. We also have PolyPhen predictions for human.

• 207 views • link
written by Emily Emily

Hi Emily,

I had a follow-up question for you about running SIFT in the dog. I see here that it should be possible, and I see that SIFT is available on Ensembl's web page for the dog. I'm running VEP locally on our cluster as recommended, but when I add the --sift flag to my command prompt, I get an error message that SIFT doesn't exist for this species. Is there a separate database I need to download? I also tried running VEP without the --cache option to force the command line to use Ensembl's server, but I still got the same error message.

Any suggestions on how to get this running from the command line?

Thanks!

• 0 views • link
written by steven_friedenberg • steven_friedenberg

Please do not cross-post to BioStar and Ensembl helpdesk.

• 1 views • link
written by Emily Emily

For SIFT, I believe the tools they list at the bottom of their Page you may be able to do non-human proteins. Especially if you pre-construct a multiple sequence alignment for a specific protein of interest. PolyPhen2 I think does have experimental support for non-human organisms, but I think only in the stand-along version you can download, not on their web interface. PROVEAN, also from JCVI like SIFT, can do predictions for any organism.

• 1,157 views • link
written by DG DG

Log in to answer this question.

More posts like this