Script to detect mismatches and indels in BLAST report
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7.5 years ago
alielbehery ▴ 10

Hi!

I am trying to find antibiotic resistant reads in 454 metagenomic datasets. The problem is that resistance against certain antibiotics e.g. fluoroquinolones and rifampin is conferred though mutations in certain genes e.g. rpoB, gyrA etc...

Mutations reported in literature are usually listed in reference to E. coli coordinates. Therefore, I made a local BLAST between reads identified to be part of rpoB, gyrA, gyrB etc... and their respective E. coli genes.

Now, I am looking for a tool/script that can help me identify mismatches or indels in these BLAST results and match them with the mutations reported in literature (I made a list of these).

I know that BioPerl can help parse BLAST output, but I don't want to reinvent the wheel. I would appreciate it if anybody could tell me about such a tool or anything similar. this would be of much help.

Thank you all in advance!!

bioperl parsing mutations blast script • 2.4k views
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what's your input ? what does your list of SNP , the blast output look like ?

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My mutation list looks like:

Gene_name codon position (E. coli) Prev_aa new_aa
rpoB      518                      N       T

My BLAST output is the default BLAST report from blastall. I can of course convert it to other formats if it would make a difference.

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65 views so far and still got no answer.

Hey guys! come on!! Isn't there anybody who is willing to help?

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