[Biopython] annotation help

[Adrian Johnson]

Hi :

I have mutation results in VCF format.

Typically I want to take

chromosome     position       reference base       consensus base

      chr21          30576509	               C                     Y (C/T)



>From this data:

1. I want to find out if this is a missense mutation.
2. Amino acid change ( VAL to MET)
3. Protein position
3. Gene name (KRTAP24) and RefSeq transcript name (NM_****)
4. Name of drug that acts on this.


Is it possible to get such annotation through biopython?


Dear Sean: You are very active in both bioconductor and biopython and
you might have worked exome-seq data and worked through this problem.
I could do this kind of stuff using SeattleSeq, however I want to get
a stand-alone program that will help getting this done locally.   what
is your opinion on this kind of problem. Are there any standalone
programs now in addition to Duke Sequence Variant Analyzer or
SeattleSeq?


thank you.

-Adrian.