[Biopython] annotation help

[Sean Davis]

Hi, Adrian.

See:

annovar
snpEff
Ensembl Variant Effect Predictor
others....

None of these (or any program that I know of) will include the name of
the drug that acts on the gene, but that information can be gleaned
from other sources once you have the gene names.  If you want to build
something from scratch, you could start with this if you are working
in cancer:

https://wiki.nci.nih.gov/display/ICR/Cancer+Gene+Index+End+User+Documentation

There are commercial softwares that offer gene/compound information,
but I do not know which is "best".

Sean


On Fri, Sep 23, 2011 at 3:12 PM, Adrian Johnson
<oriolebaltimore at gmail.com> wrote:
> 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.
>