Getting the genomic positions for a set of protein sequences

Question

[ahmad]

Hi,

I have a fasta file of protein sequences belonging to a known species. My goal is to retrieve the genomic coordinates for each protein sequence. I'm using blastp where I have my protein sequences as query and searching against protein database of the known species. Blastp was successful in mapping those query sequences to known regions, however, it doesn't give any information about the genomic positions of those proteins.. Is it possible to do this using blastp? If not, could you recommend any tool to do that?

[GouthamAtla]

tblastn ? Or UCSC BLAT ?

Answer 1

[glihm]

Hi,

First question, are you working with command line or online requests?

Using tblastn from NCBI server, if there is a match well characterized you have ALL the genomic information clicking on the sequence ID (Which chromosome, region, position etc...). Otherwise, BioPython parsers allow you to recover this information in output files if the targeted sequences are described.