Converting mRNA coordinates to chromosome coordinates

[david.tamborero]

hi,

any of you know how to (easily) change mrna coordinates of a gene to chromosomal positions (or viceversa)? Something as (figures are invented): KRAS c.819A>T to chr12:25,357,800 A>T

I just need it from time to time in specific cases, so the simplest the better.

many thanks!
david

[dpryan]

Hopefully there's a website out there that will do that for you, but if not, you can use the transcriptLocs2refLocs() function in GenomicRanges (an R package from Bioconductor).

[david.tamborero]

Thanks for your answer!

FYI, the package -at least in my R libs installation- is in library('GenomicFeatures')

Anyway, I quickly check the command and it seems to require that I indicate the genomic coordinates of each exon (of each transcript) and therefore the position of the mrna I am interested in, so the 'only' thing that the program does is to use this info to perform the conversion.

I would love something that do not require to input more info than just the name of the gene and the mrna position...

[david.tamborero]

I mean, I notice that I can retrieve this info from another commands of the package, so I will do it (or using other means, as the Ensembl api) if no easier way to do that exists in some magic website or so.

thanks again!
david