How to extract the mismatched unique region from Mauve ?

Question

[k.kathirvel93]

Dear all, Now, i am working in the field of comparative genomics, and am using mauvealigner to find the unique regions of my bacterial draft genomes, example : Genomic islands . I had aligned my draft genome against with the suitable reference genome and i got some mismatched unique regions in my draft. Now i want to extract that specific unique regions in the .fasta format from mauve. How i can do that, need your suggestions. Thanks in advance.

K.Kathir

Answer 1

[Sej Modha]

In past, I have used following script to convert xmfa to fasta. https://github.com/lskatz/lskScripts/blob/master/convertAlignment.pl