Obtain Genomic Position From Codon # & Refseq
2
0
Entering edit mode
9.7 years ago
Raymond301 ▴ 160

I have a large list of mutations, their codon # and I can map through the gene to a RefSeq Id (include the transcript version).

I'd like to find the genomic position from this information, I would think that there is some API or tool, I'm still picking through Bio:Perl to see if there is anything there.

But does anyone know of any API available that can help me?

refseq • 3.2k views
ADD COMMENT
0
Entering edit mode

You say you have the codon number. Does that mean you don't have the exact nucleotide position in the RefSeq mRNA?

ADD REPLY
0
Entering edit mode
9.7 years ago
Bert Overduin ★ 3.7k

Assuming that you have the exact position of your mutations in the RefSeq sequences, you can use Ensembl's Variation Effect Predictor (VEP) to get the genomic position of your mutations plus lots of additional information. You can input your mutations in HGVS format (e.g. NM_153681.2:c.7C>T). At the moment the web interface does not support input of RefSeq-based variants, but the standalone Perl script, which is very easy to use, does. We have extensive documentation on how to install and use the VEP script. In case you need any help or additional information, please don't hesitate to contact the Ensembl helpdesk at helpdesk@ensembl.org. One thing to note though is that RefSeq cDNAs do not necessarily always map perfectly to the reference genome assembly, as they exist independently from this.

ADD COMMENT
0
Entering edit mode
6.2 years ago
Reece ▴ 310

Consider the Python hgvs package. [Disclosure: I'm one of the authors.]

ADD COMMENT

Login before adding your answer.

Traffic: 2696 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