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Orient and rotate mitochondrial genome #25

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sjackman opened this issue May 17, 2018 · 2 comments
Open

Orient and rotate mitochondrial genome #25

sjackman opened this issue May 17, 2018 · 2 comments
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@tseemann
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@sjackman
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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?
@tseemann tseemann self-assigned this May 21, 2018
@tseemann
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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.

@sjackman
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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).

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@sjackman @tseemann