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Published 20 hours ago • verified publisher icon tseemann

Orient and rotate mitochondrial genome

Open sjackman opened this issue 6 years ago • 2 comments

I have an animal mitochondrial genome assembled by Unicycler (so no overlap). I'd like to orient and rotate the genome to agree with its closest relative in Genbank. I have a FASTA file of the related genome. Is this task possible with Berokka?

sjackman avatar May 17 '18 23:05 sjackman

No, I currently have no orientation support.

I'm not even sure if circlator can do it for an abritrary DNA sequence - i think it needs an ORF and it does tblastn.

tseemann avatar May 21 '18 05:05 tseemann

Yeah, I look into circlator too, and came to the same conclusion. I checked and my genome does not start with a coding gene, a tRNA I think (I could confirm).

sjackman avatar May 21 '18 16:05 sjackman