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Polyphen-2 shum1 Bioinformatics 4 06-03-2013 04:20 PM
help with polyphen output kjaja Bioinformatics 1 02-25-2012 09:19 AM
PolyPhen-2 strange Job Queue System lshen Bioinformatics 0 12-07-2011 04:14 AM

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Old 09-26-2010, 08:11 AM   #1
yuanzhi
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Location: New York

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Default how to use polyphen-2

Dear All

I was trying to use PolyPhen-2 to predict SNP function effect. I generated my batch file as below

chr1:155078890 G/T
chr1:165363783 A/G
chr2:47864062 A/C
chr2:47876619 C/C
chr3:71886710 G/T
chr3:71886711 A/T
chr3:197099773 A/G
chr4:1771285 A/G

and uploaded them to PolyPhen-2's Batch Query webpage http://genetics.bwh.harvard.edu/pph2/bgi.shtml. But after running the job for more than 5 hours, the Grid Gateway Interface page showed an error for my job and stopped it.

Maybe I didn't use it properly? Can anyone help me on this? Thanks very much in advance.

-YZ
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Old 09-27-2010, 04:21 AM   #2
svl
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Hi yuanzhi,

I've found the performance and errors of polyphen2 confusing as well. But for your genomic positions it might be because they are not in protein coding sequence (I only checked your first btw, chr1:155078890 G/T), and polyphen2 is "a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein" as they say themselves

If that's the case though, it should in my opinion tell you that in a clear error message... So maybe someone else has a better explanation

Last edited by svl; 09-27-2010 at 04:28 AM.
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Old 10-09-2010, 04:17 PM   #3
iadzhubey
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Dear yuanzhi,

Your batch format looks perfectly valid. Can you tell me what kind of error message you received? Please feel free to contact me directly via email (I am PolyPhen-2 developer).

--Ivan
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Old 10-22-2010, 01:36 AM   #4
shum1
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hi,

Anyone who has worked with the standalone application of polyphen2???

Last edited by shum1; 10-22-2010 at 01:54 AM.
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Old 10-22-2010, 07:18 AM   #5
iadzhubey
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Quote:
Originally Posted by shum1 View Post
hi,

Anyone who has worked with the standalone application of polyphen2???
If you have any questions about PolyPhen-2 please e-mail me.

Best,
Ivan Adzhubey <[email protected]>
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Old 11-22-2010, 08:10 AM   #6
flyinflute
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Default same question

I am a user of pph2, I find that the user guide in the wiki page can not be found, there are links, but no documents. how can I get a manual of pph2. is there anyone else use it, I would like to communicate with all of you, thanks, my email: [email protected]
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Old 11-22-2010, 11:55 AM   #7
bioinfosm
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Quote:
Originally Posted by iadzhubey View Post
Dear yuanzhi,

Your batch format looks perfectly valid. Can you tell me what kind of error message you received? Please feel free to contact me directly via email (I am PolyPhen-2 developer).

--Ivan
Thanks for the tool Ivan.

Curious if you could point to the latest in such predictor tools and any standardized comparisons with the likes of PMUT and SIFT.
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Old 11-22-2010, 07:49 PM   #8
iadzhubey
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Quote:
Originally Posted by bioinfosm View Post
Thanks for the tool Ivan.

Curious if you could point to the latest in such predictor tools
This is a good starter:

http://www.gen2phen.org/wiki/prediction-tools

Quote:
Originally Posted by bioinfosm View Post
and any standardized comparisons with the likes of PMUT and SIFT.
You may want to check the CAGI website:

http://genomeinterpretation.org/

Note, truly FAIR and ACCURATE comparisons is an extremely hard task and not many of the developers of such tools are interested in spending (should I say wasting?) their time on this.

--Ivan
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Old 03-21-2011, 11:46 PM   #9
Buzz0r
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Hi,

i am also working with the standalone version x23 of P2.
we have some problems with it when lock files are not completely removed from the scratch library on our cluster. this will probably only need a small tweak but maybe you can give me ahint ivan?

also i get error messages for some genes and it doesnt give a prediction but i will send it straight to you ivan, now that we have our pipeline upgraded to hg19 and the newest databases i need to fix this problem...
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