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6.4 years ago
prittam32
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0
Suppose I have the genomes of two organisms stored in variable 'a' and 'b'. I want to BLAST them against each other and store the identity percentage in another variable 'c'. I'm new to Biopython. Can anyone please provide me the code my which I can solve this problem.
You won't get a single percentage identity with BLAST - what do you want to do with multiple numbers?. BioPython itself is also probably not the best way to go about this. Can you not make use of a commandline tool?
Thank You for your reply. I have a list containing the genome sequences of 10 different organisms. I will make another list of antibiotic resistance gene sequences and check their presence in each genome using BLASTn. I tried pairwise2 but it goes out of memory. So i tried splitting genomic sequence into various overlapping sequence. Although it works, It is very time-consuming. So I wish to use BLASTn to reduce the time.
It should be feasible to blast each ARG against each genome sequence, one genome at a time.
Please share the code you’re currently use?