cDNA or protein location to genomic DNA location

[Liam_Gallagher]

Hi all,

I have a list of protein mutations and cDNA mutations and I would like to obtain the original genomic locations. Is there a tool to convert the location from cDNA or protein (maybe providing in input the correct isoform...) to the genomic location ?
Thank you very much,

Cristian

[Liam_Gallagher]

I know that some tools (e.g. Ensembl Variant Effect Predictor..) can predict the effect of a DNA mutation (providing in input a list of genomic coordinates of the variants) on transcripts and proteins....but i never heard about something working on the other direction....from protein to genomic DNA.... thank you

[Richard Finney]

Liam G., Don't Look Back in Anger, try blat :

http://genome.ucsc.edu/FAQ/FAQblat.html#blat1

and

http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

Please set query type to "protein"

Use the web version to get comfortable with blat.

If you have a lot of data, you can download BLAT and use the command line version.

[Liam_Gallagher]

Thanks Richard for the quick reply!
ahah I think Blat is gonna be the tool who saves me...and after all will be my Wonderwall! :-) hope you like Oasis.... :-)
Thank you very much, i will try!!

[Liam_Gallagher]

Unfortunataly Blat requires in input the amino acidic sequence....but I only have the position of the mutated AA. I know how to get the AA sequence but I was looking for an automatic method...any ideas are welcomed!
Thanks

Cristian

[ymc]

You can download RefSeq exon intron boundaries of the transcriptome from somewhere. Then you should be able to write a simple program to map the positions to genomic positions.