How to find strain specific truncated genes?
Hello,
does anyone know a good software/method to identify truncated genes among a set of closely related bacterial genomes?
I have to find a strain specific feature that allows me to discriminate a strain from all the others belonging to the same species, so I thought picking a gene of different length would be a simple PCR test. I used Mauve to identify large indels but when I checked them with other software they were not always reliable.
Thanks!
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Just a suggestion would be to try assembly and then annotate with Prokka and compare the annotation between strains for specific/missing/truncated genes. I was able to do that for teaching purposes and get a few known genes present/absent between similar pathogenic v.s non-pathogenic bacteria.