Question: Using Standalone Blast In Biopython
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gravatar for midox
3.3 years ago by
midox250
Tunisia
midox250 wrote:

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.

ADD COMMENTlink written 3.3 years ago by midox250

If you only have two sequences, use pairwise2, also with biopython.

ADD REPLYlink written 3.3 years ago by st.ph.n2.5k

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?

ADD REPLYlink written 3.3 years ago by midox250

I needing to find the best alignment between different frame translations. Some biostars users were able to help me out. See this post.

ADD REPLYlink written 3.3 years ago by st.ph.n2.5k

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

ADD REPLYlink written 3.3 years ago by midox250

Since you're stuck on BLAST, I would run BLAST from the command-line, using the flag -max_target_seqs 1 and -oufmt 6 to 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.

ADD REPLYlink written 3.3 years ago by st.ph.n2.5k

sorry i don't understand. can you explain me your response please

ADD REPLYlink written 3.3 years ago by midox250

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.

ADD REPLYlink written 3.3 years ago by st.ph.n2.5k
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