I am wondering if there is a program or online tool to get protein residues and residue #s within their parent protein simply by inputting its respective DNA chromosomal coordinates. For example, if I have a range chr22:18003539-18004115, I want to be able to get the genes within that locus, the protein accessions coded for by those genes, and the residues and residue #s themselves. I tried the Mapback tool, but it doesn't seem to properly match up residue #s. Any suggestions?
2 answers
My solution (without having to write additional code):
Use the Mapback tool to get residues (e.g. 1 Met) and protein accessions (e.g. NP_958440) from chromosomal coordinates (e.g. chr7:55086971 - 55086973)
Use the bioDBnet:db2db tool to get gene IDs (e.g. 1956 or EGFR) from protein accessions
note: I haven't yet figured out a way to access the Mapback results programmatically to get protein accessions, but URL parsing may work.
Besides the solution provided by Pierre ( http://www.biostars.org/post/show/43442 ), I also suggest the Ensembl Perl API, the tutorial is a good point to start: http://ensembl.org/info/docs/api/core/core_tutorial.html
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duplicate of http://www.biostars.org/post/show/43442?
I tested out the Bioconductor packages -- is there a way to get protein accessions as well, so I can divide CDS number by 3 (and if cds%3!=0, round up) in order to get the AA residue?
On second thought, I can just use Mapback -- which does work most of the time -- and input the resulting RefSeq accessions into bioDBnet to get the gene IDs.
could you please add this as an answer - it helps designating questions that have some answers