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2.4 years ago
eli_bayat
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90
Hello, I m working on variant detection in a bacteria. I know from literature that a mutation occurred on a gene in bacteria of interest at a position according to the E.coli numbering system. How can I convert this number to the mutation position in my bacteria. For example, if there is a mutation from G to C at position 1064 according to Ecoli numbering system, what position it translate to, in the bacteria?
I have seen suggestions such as alignment of the bacteria to Ecoli, but not sure if there is a better way to do this.
Any help appreciated
I have the same problem, can you give me the solution if you have it?
I ended up aligning the bacterial genome to E.coli genome and find the position in bacteria correspond to the reported position in E.coli. I used mafft for this.
Thanks, I will try the mafft tool for the alignement.