How do I find the gene name with the allele number from the databases?
0
0
Entering edit mode
26 days ago

How do I find the gene name with the allele number from the databases?

rna-seq • 196 views
ADD COMMENT
1
Entering edit mode

Provide examples whenever any sort of identifiers are being mentioned. Without that information there is no way to answer this question.

ADD REPLY
0
Entering edit mode

X_84670461

ID chr- SNP position 26_23089878 How do I find the gene name with the allele number from the databases?

ADD REPLY
0
Entering edit mode

I don't immediately see a connection between the two examples you provided. What is X_84670461 and how is it related to 26_23089878? What genome is this from?

e.g. If we were looking at a SNP rs1593939233 then you can find the gene name and the allele frequency by using EntrezDirect like this:

$ esearch -db snp -query "1593939233" | esummary | xtract -pattern DocumentSummary -element NAME,FREQ,DOCSUM
BRCA2   A=0.5/1 HGVS=NC_000013.11:g.32381866A>G,NC_000013.10:g.32956003A>G,NG_012772.3:g.71387A>G,NG_056630.1:g.375A>G|SEQ=[A/G]|LEN=1|GENE=BRCA2:675
ADD REPLY

Login before adding your answer.

Traffic: 1355 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6