Question: Help To Blast Sequences Against Drosophila Genome In Biopython
0
gravatar for nikhil.joshi92
6.0 years ago by
nikhil.joshi920 wrote:

Hi,

I am trying to blast certain sequences (in fasta files) against the drosophila genome using the qblast operation provided in BioPython. From the documentations, I have figured out that the second argument that you are supposed to enter in qblast refers to the database against which you are trying to BLAST. I went through the BioPython documentation, but wasnt able to understand how to blast against the drosophila genome. That is, I couldn't figure out the specific (second) argument that I need to enter in qblast to BLAST against the drosophila genome. Can someone provide me an example that shows how to BLAST against the drosophila genome using the NCBIWWW.qblast tool?

Thanks!

biopython blast • 3.0k views
ADD COMMENTlink modified 6.0 years ago by Steve Moss2.2k • written 6.0 years ago by nikhil.joshi920
0
gravatar for Steve Moss
6.0 years ago by
Steve Moss2.2k
United Kingdom
Steve Moss2.2k wrote:

This is basically just a wrapper around the web QBLAST server. If you view the source you can see what it does http://biopython.org/DIST/docs/api/Bio.Blast.NCBIWWW-pysrc.html. If you want to BLAST against the Drosophila melanogaster reference genome, I believe you should set database='refseq_genomic' and add an extra parameter organism='7227' where 7227 is the taxonomic ID for Drosophila melanogaster.

Something like:

dmel_qblast = NCBIWWW.qblast(program="blastn", database="refseq_genomic", sequence=input_sequence, organism="7227")

ADD COMMENTlink written 6.0 years ago by Steve Moss2.2k

Perhaps there has been a change since on NCBI's side since this posting, but the correct way to do this would be through the "entrez_query" argument:

NCBIWWW.qblast(program="blastn", database="refseq_genomic", sequence=input_sequence, entrez_query="txid7227[ORGN]")
ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by saladi120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 770 users visited in the last hour