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!