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Improve ORF coordinates detection #22

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Donaim opened this issue Jul 25, 2024 · 1 comment

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Donaim commented Jul 25, 2024

Instead of doing global alignment on whole genome sequences, align just the searched subtype ORF sequence to the full query sequence.

The searched subtype ORF sequence should be prefixed and suffixed with "+" to discourage spread of nucleotides.

Donaim added the enhancement label

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Donaim commented Jul 25, 2024

The initial approach failed because of weird mafft behaviour.

Currently it seems like integrating mappy instead of mafft for this would be the best approach.

Need more investigation.

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