[Biopython] annotation help

[Adrian Johnson]

Thanks Sean. I will look into those software you mentioned.
-Adrian.

On Fri, Sep 23, 2011 at 3:33 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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.
>>
>