This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Polyphen-2 Batch

I would like to run 189 SNPs through Polyphen-2 using the Batch Query facility. I submitted a job that has been sitting on the queue for over 4 days. I used the following settings:

Classifier: HumDiv Assembly: NCBI36/hg18 Transcripts: Canonical Annotations: Missense

I have no trouble submitting SNPs on the dbSNP Query page.

Does batch work on Polyphen-2? Or am I doing something wrong?

snp
• 5,756 views • link
updated by Bamyasi Bamyasi • written by Gary B. Lipton • Gary B. Lipton

2 answers

Batch does work but their server was in "extreme" load last Friday. Maybe they are having server issues, also 189 is not that many SNPs which makes me think your job is just getting repeatedly getting pushed to the bottom of the stack.

• 0 views • link
written by Zach Stednick Zach Stednick

Thanks for the info. The job submitted on 4/21 is still on the queue, so whether it is the load or server problems, it is still effectively unavailable. I am looking at other options. NIEHS SNPinfo provides the TOLERATED/DAMAGING classification, but does not provide the Polyphen score. If there are any other tools or servers that provide the Polyphen score, please post them.

• 0 views • link
written by Gary B. Lipton • Gary B. Lipton

Hi Gary,

Why not e-mail PolyPhen-2 server maintainers (that's me ;-) with your problem? Our compute backend is currently experiencing long delays due to large number of enormous size batches submitted vi web interface (we are talking billions of queries). We are working on a solution right now but please understand that our resources are limited. Please contact me via e-mail directly and I am sure will be able to help you with your particular batch in the meantime.

• 0 views • link
written by Bamyasi Bamyasi

Log in to answer this question.

More posts like this