Obtain Genomic Position From Codon # & Refseq

Question

[Raymond301]

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?

[Bert Overduin]

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

Answer 1

[Bert Overduin]

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 [e-mail]. 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.

Answer 2

[Reece]

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