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7.3 years ago
midox
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290
Hello, i would like some help in using Blast in Biopython. Can you give me an example of using Blast in Biopython ? for example two DNA sequences. my problem is: i have two DNA sequences and i would like to do an alignment between these two sequences so i would use BLAST in Biopython but i don't know how use BLAST under Biopython. Can you help me please? Please DO NOT post the biopython tutorial (http://www.biopython.org/DIST/docs/tutorial/Tutorial.html) because I've already gone through it and everyone seems to refer to it.
Thank you for your responses.
If you only have two sequences, use pairwise2, also with biopython.
yes! i can use the pairwise2 but i need the best alignment. In BLAST, usually i use the e-value parameter. have you an idea in pairwise2 what's the e-value parameter??? the score of alignment maybe?
I needing to find the best alignment between different frame translations. Some biostars users were able to help me out. See this post.
thank you. But if i have the same score? what's a solution? in my case i need a threshold to accept the alignment between two sequences. so in this case what's the threshold should i choose in your exeperience please? Thanks
Since you're stuck on BLAST, I would run BLAST from the command-line, using the flag
-max_target_seqs 1and-oufmt 6to give you the best sequence per query in a tab-delimited output, that would be very easy to parse with further unix cmds, or with a python script.sorry i don't understand. can you explain me your response please
what have you tried in biopython to run blast, and parse your results? I can show you how to run blast in biopython, but you don't want that. so i recommend running a standalone blast outside of python, and then choosing a method to parse your results.