Map Uniprot On Genomic Coordinates (Eg. Hg19)

Question

[jirivoller]

Hello, what is the easiest way of mapping uniprot records into genomic coordinates (eg. hg19)? Preferably using R+bioconductor.

I just tried to do so using knownGene table (giving exon and cds positions) from uscs mysql database but this is not the way. - uniprot IDs are sometimes assigned to more exon sets (Q00987=MDM2 ) and calculated protein lengths tend to differ by a couple of AKs from uniprot records.

Thank you for your suggestions

Answer 1

[Sean Davis]

There are many aligners that can do this ranging from BLAST to blat. I'd suggest giving one of those a try. Bioconductor has many useful tools related to NGS, but aligning proteins to a genome is not (yet) one of its strengths. That said, it would be straightforward to wrap blat, for example, in a small R function to perform the analysis from within R.