Question: How To Blast Against A Local Database
1
gravatar for mealbahrani
7.6 years ago by
mealbahrani10
mealbahrani10 wrote:

I want to BLAST an mRNA reference sequence against a local database in my directory (a collection of RNA reference sequences) using a BioPython program. I know how to perform BLAST against online database such as NCBI database using the following code:

from Bio.Blast import NCBIWWW

sequence = """GGAGGATATATTCAAC"""

blast_handle = NCBIWWW.qblast('blastn', 'nr', sequence)

    blast_handle.seek(0)
    blast_file = open('blast-output.xml', 'w')
    blast_file.write(blast_handle.read())
    blast_file.close()

But my question is how to do BLAST against a local database in my directory?

local database biopython blast • 12k views
ADD COMMENTlink modified 6.7 years ago by Biostar ♦♦ 20 • written 7.6 years ago by mealbahrani10
6
gravatar for David W
7.6 years ago by
David W4.8k
New Zealand
David W4.8k wrote:

This is covered in the Biopython tutorial under the heading "Running BLAST Locally". You'll need to install the BLAST executables, then follow the examples. If you'd prefer, you can run the create your databases and run your BLASTs via the command line, then use Biopython to parse the resulting xml.

ADD COMMENTlink written 7.6 years ago by David W4.8k
2
gravatar for Bioch'Ti
7.6 years ago by
Bioch'Ti1.0k
France (Avignon)
Bioch'Ti1.0k wrote:

You can also use PrfectBlast, a GUI that perform this task whatever your platform is: http://code.google.com/p/prfectblast/ Easier to handle for people that do not use python/perl.

ADD COMMENTlink written 7.6 years ago by Bioch'Ti1.0k
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