Question: How to find identity percentage of two genomes sequences stored in two variable by carrying using BLAST in biopython
gravatar for prittam32
7 months ago by
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 • 205 views
ADD COMMENTlink modified 7 months ago by ATpoint30k • written 7 months ago by prittam320

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 7 months ago • written 7 months ago by Joe16k

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 7 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 7 months ago by Joe16k
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