Biopython Local Blast Giving Mega Blast Results

Question

[muneezapatel]

Hello Everyone, I am trying to use the stand alone local blast in python to return back to make the blast results of particular sequences. It works but when I tally my results with the online version of blast it seems like the standalone blast is returning to me the "megablast- highly similar sequences" instead of blastn - somewhat similar sequences which is what I want.

This is my code:

 result_handlel= NcbiblastnCommandline(query="l70.fasta", db = "MG1655", out = 'resultl.xml', outfmt= 5, evalue = 0.0001)
    os.system(str(result_handlel))

Do you have any idea why it is doing this? It is the blastn command line so it makes most sense for it to return blastn results.

Thank you!

[Peter]

Note NcbiblastnCommandline(...) does not give you a handle so storing it in a variable called result_handlel is a bit odd. Also you can invoke it directly with:

stdout, stderr = result_handlel()

Answer 1

[Andrzej Zielezinski]

In BLAST+ the default program for blastn is megablast. To switch to regular blastn just add keyword argument task="blastn" to your command:

 result_handlel= NcbiblastnCommandline(query="l70.fasta", db = "MG1655", out = 'resultl.xml', outfmt= 5, evalue = 0.0001, task="blastn")