CODEWITHSUNDEEP
pythonbioinformaticsbiopythonblast
Ashutosh Anand
Ashutosh Anand

Reputation: 11

How to automate multiple BLAST runs online?

I have the proteome of a bacteria in a FASTA file. Now, I want to run BLAST on individual protein with an antigen protein online. However, due to the large size of the proteome, running BLAST individually is cumbersome. What can I do to automate this process? I have some knowledge of Python but I am unable to make a pipeline to automate the process.

Upvotes: 1

Views: 638

Answers (1)

Padix Key
Padix Key

Reputation: 970

Biotite, a package I am developing, has an NCBI BLAST interface: https://www.biotite-python.org/apidoc/biotite.application.blast.BlastWebApp.html

You could simply loop over all your sequences you would like to BLAST. However, the usage rules by the NCBI restrict each user to one BLAST job per 5 minutes, so it might run pretty long.

As I understand, you have just one protein reference sequence (the antigen), am I right? In this case it is probably easier to run a Smith-Waterman alignment for each query locally on your computer: https://www.biotite-python.org/apidoc/biotite.sequence.align.align_optimal.html

Upvotes: 1

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