[Bioperl-l] NCBI/Swissprot cross-ref

[Ewan Birney]

On Thu, 2 Dec 2004, Fontaine, Burr R wrote:

> Hi,
>
>
>
> Does anyone know if BioPERL can help me cross-reference gene and SNP
> ID's between NCBI and Swissprot? I can't find anything at NCBI or
> Swissprot that does this directly.
>

Do you mean SNP ids to Variation IDs in Swissprot? In the swissprot files
some variations do have dbSNP ids (I believe in the feature table) and I
think there is a goal to get this done better in the future in swissprot.


Swissprot definitely holds many more variants which are just mentioned in
papers, which are often the ones with phenotypic effects.



>
>
> The closest thing we've found so far for this is the kgxref table at
> UCSC, but this table does not includes SNP's. Also, this table appears
> to include Swiss-prot ID's for both proteins and genes in the same
> field, and I'm not sure how to sort these out.
>
>
>
> #kgID       mRNA        spID        spDisplayID geneSymbol  refseq
> protAcc     description
>
> AY231461    AY231461    AAO84335    AAO84335    TAZ         NM_000116
> NP_000107   Tafazzin exon 5 deleted variant long form.
>
> AY231462    AY231462    AAO84336    AAO84336    TAZ         NM_000116
> NP_000107   Tafazzin exon 7 deleted variant long form.
>
> AY231463    AY231463    Q86XR0      Q86XR0      TAZ         NM_000116
> NP_000107   Tafazzin exon 5 and exon 7 deleted variant long form.
>
> AY258036    AY258036    Q86XQ9      Q86XQ9      TAZ         NM_000116
> NP_000107   Tafazzin short form.
>
> AY258037    AY258037    Q86XQ8      Q86XQ8      TAZ         NM_000116
> NP_000107   Tafazzin exon 5 and exon 7 deleted variant short form.
>
> AY258038    AY258038    Q86XQ7      Q86XQ7      TAZ         NM_000116
> NP_000107   Tafazzin exon 7 deleted variant short form.
>
> AY258039    AY258039    Q86XQ6      Q86XQ6      TAZ         NM_000116
> NP_000107   Tafazzin exon 5 deleted variant short form.
>
> BC005062    BC005062    Q7Z6N8      Q7Z6N8      TAZ         NM_000116
> NP_000107   Tafazzin, isoform 5.
>
> BC011515    BC011515    Q96F92      Q96F92      TAZ         NM_000116
> NP_000107   Similar to tafazzin (cardiomyopathy,   dilated 3A
> (X-linked), endocardial fibroelastosis 2, Barth syndrome).
>
> X92762      X92762      Q16635      TFZ_HUMAN   TAZ         NM_000116
> NP_000107   tafazzin (cardiomyopathy, dilated 3A (X-linked); endocardial
> fibroelastosis 2; Barth syndrome)
>
>
>
> Thanks in advance for your help.
>
>
>
> Burr Fontaine
>
>
>
>