[Bioperl-l] NCBI/Swissprot cross-ref

[Sean Davis]

Burr,

You can simply use the ucsc table browser to find the overlap of SNPs with 
genes by doing an intersection.  Note that for human, only the July 2003 
build has a SNP table right now.  Perhaps in the next week, I think, they 
will have the SNP table in the 2004 build (build 35).

Sean

----- Original Message ----- 
From: "Fontaine, Burr R" <bfontain at iupui.edu>
To: <bioperl-l at portal.open-bio.org>
Sent: Thursday, December 02, 2004 1:42 PM
Subject: [Bioperl-l] NCBI/Swissprot cross-ref


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.



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







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