Question: How to find identity percentage of two genomes sequences stored in two variable by carrying using BLAST in biopython
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gravatar for prittam32
14 months ago by
prittam320
prittam320 wrote:

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.

biopython alignment python gene • 310 views
ADD COMMENTlink modified 14 months ago by ATpoint38k • written 14 months ago by prittam320
1

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?

ADD REPLYlink modified 14 months ago • written 14 months ago by Joe17k

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.

ADD REPLYlink written 14 months ago by prittam320

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?

ADD REPLYlink written 14 months ago by Joe17k
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