[BioPython] RV: variations in a mRNA (was EUtils)

[Bonis Sanz, Julio]

I sent a message to NCBI Help desk and they responded this. No so much help, but I will try to understand now how biopython works with elink to try to solve my problem.



-----Mensaje original-----
De: Gabrielian, Andrei (NIH/NLM/NCBI) [mailto:gabrieli at ncbi.nlm.nih.gov]
Enviado el: miércoles, 10 de noviembre de 2004 1:19
Para: Bonis Sanz, Julio
Asunto: RE: variations in a mRNA


Dear NCBI user,

if you click on Links -> SNP for this sequence, you'll be linked to 310
SNPs:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=Display&dopt
=nucleotide_snp&from_uid=10835174

the same result you'll get if you do this via e-utilities call:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nucleotide&db
=snp&id=10835174

Hope this helps,
NCBI Help desk


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Dear Sirs, 

I am building an application that tries to retrieve all the SNPs contained
in a 
given gene.

I am using this URI:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=10
8351
74&rettype=gb&extrafeat=1

that is the gene for HTR2A human receptor....

I only get 7 variations (SNPs)... 

But if you go to 

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=3356&mrna=NM_000621&ctg=
NT_0
24524&prot=NP_000612&orien=reverse&view+rs+=view+rs+&chooseRs=all

You can see that there are several more SNPs (intron ones and synonims ones
for 
example).

What I want is to retrieve by EUtils ALL the SNPs in a given gene, but I am
not 
sure of the parameters to send to the EUtils 

Any help will be appreciated.

Julio Bonis Sanz MD
Research Group on Biomedical Informatics GRIB: http://www.imim.es/grib/


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