Change genbank files orientation to '5 > '3 based on their ORF direction

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3.5 years ago

Balazs Horvath ▴ 10

Hi fellows,

Does anyone have an idea / script how to reverse complement a large number of annotated viral genbank files (generated by metagenomics de novo assembler) based on if their ORFs "reversed" '3 > '5 direction? Of course if the ORF is 5' > 3' direction no RC is needed, in such case there would be no operation on the sequence. Fortunately this kind of single segmented virii usually has only one ORF if not, all of them pointing the same direction.

Balázs

reverse genbank ORF complete • 601 views

ADD COMMENT • link updated 3.5 years ago by Joe 21k • written 3.5 years ago by Balazs Horvath ▴ 10

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You mean you just want to flip the sequence essentially (so that bottom strand ORFs are shown as top strand)?

I don't know this virus, but I would assume it will have both forward and reverse orientation ORFs, so can you clarify what you mean by

based on if their ORFs "reversed" '3 > '5 direction?

...since it will have both surely?

ADD REPLY • link 3.5 years ago by Joe 21k

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