Polyphen-2

[shum1]

Hi everyone, Is there anyone who has worked with the Polyphen-2 standalone application??

[shum1]

I have some problems working with this. Please If someone has worked with it, guide.

[iadzhubey]

I have some problems working with this. Please If someone has worked with it, guide.

E-mail me your questions.

Best,
Ivan Adzhubey <[email protected]>

[rpauly]

Hi,

Polyphen2 is a great tool for SNP annotations, works great with dbSNP annotations too!
For one of our projects we were trying to identify the dbSNP database version used...is it dbSNP137?

If so, is there a way we could download the database you use for the annotations?

Thanks much!

[iadzhubey]

Hi,

Polyphen2 is a great tool for SNP annotations, works great with dbSNP annotations too!
For one of our projects we were trying to identify the dbSNP database version used...is it dbSNP137?

If so, is there a way we could download the database you use for the annotations?
Thanks much!

dbSNP rsIDs found in the PolyPhen-2 output are obtained from Swiss-Prot protein annotations. This is a smaller subset (about 60,000) of manually verified human dbSNP rsIDs for missense SNPs only. They are not tied to a particular dbSNP build.

dbSNP rsIDs which are found in the MapSNPs output (Batch query pipleine) are taken from UCSC Genome Browser snp135 track. These correspond to dbSNP build 135.

I am not sure I understand which database you want to download?