Mutation Taster Gdna Coordinates

Question

[jp.of.mars]

Hello all,

I want to use the script perl of Mutation Taster to make a batch analysis. The file in input ask the gdna coordinate but I have only proteic coordinates. Could you tell me how to convert Acid amine position in gDNA position for Mutation Taster ( http://www.mutationtaster.org/BatchQueries.html ) ?

Thanks !

Answer 1

[JC]

For this you need a gene annotation source, if your model is known (human, mouse, ...) you can use Ensembl, UCSC, etc to convert your coordinates (some scripting will be required, perhaps). If not, well, you need to map your peptides to your reference genome or assembly, you can use tblast for that.

Answer 2

[jp.of.mars]

I try to use GeneMapper, from Bioperl, but I don't understand how to use it.

The problem is I dont know what is the gdna position.

For example , for BRCA1 if the codin sequence positon is 1, the cDNA position is 1791, the gDNA is 31544 and the Chromosomic position is 41245957.

The are a conversion tool on the MutationTaster site, I need Chromosomic Position to use it and to obtain gDNA position..