Question: Obtain Genomic Position From Codon # & Refseq
gravatar for Raymond301
7.9 years ago by
Rochester, MN
Raymond301140 wrote:

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 • 2.8k views
ADD COMMENTlink modified 4.4 years ago by Reece270 • written 7.9 years ago by Raymond301140

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

ADD REPLYlink written 7.9 years ago by Bert Overduin3.7k
gravatar for Bert Overduin
7.9 years ago by
Bert Overduin3.7k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.7k wrote:

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 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 COMMENTlink written 7.9 years ago by Bert Overduin3.7k
gravatar for Reece
4.4 years ago by
United States
Reece270 wrote:

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

ADD COMMENTlink modified 4 months ago by RamRS26k • written 4.4 years ago by Reece270
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