Map Uniprot On Genomic Coordinates (Eg. Hg19)
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9.5 years ago
jirivoller ▴ 10

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

coordinates mapping uniprot • 2.6k views
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Entering edit mode
9.5 years ago

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.

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