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Genome sequence from protein

I've done tblast of a certain protein and got a list of hits. Is there a way to programmatically extract genomic regions for my hits?

I'm using biopython mostly

sequence alignment genome
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written by tim.ivanov.92 • tim.ivanov.92

Are you interested in extracting a specific region of the subjects or entire fasta sequence? What sort of databases are you using? Could you post your current code?

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written by Sej Modha Sej Modha

I am interested in a specific region, the database is ncbi nr

here is is the code

from Bio.Blast.Applications import NcbiblastxCommandline
tblastn='/uge_mnt/home/tim_ivanov/soft/blast/ncbi-blast-2.7.1+/bin/tblastn'
nt_db='/uge_mnt/home/tim_ivanov/DATA/fasta/nt'
blastx_cline = NcbiblastxCommandline(cmd=tblastn, query="mrp_NM_001316390.faa", db=nt_db, outfmt=5, out="opuntia.xml")
print blastx_cline
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written by tim.ivanov.92 • tim.ivanov.92

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