Is it possible to supplement a gbk file with manual annotations?
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14 months ago

I have a viral genome gbk file that only shows the open reading frame, I wish to also annotate each ORF with the 5' and 3' UTRs that have been published in a paper so I have the coordinates in a table but I want to annotate these onto the gbk file. Is there a tool that can do this and if not, how can I produce such annotations myself?

annotation genome viral • 431 views
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14 months ago
JC 12k

The GBK is just a text document, just open it with a text editor (Vim, MS Code, Notepad++ and never WORD) and follow the syntax to add your features

However, if there are many you need to add, you will need to code something, BioPython and BioPerl can read/write GBK files

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So I can just write a script to manually insert the annotations as the desierd location? Would this be eaiser in a GFF file?

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if you respect the syntax, yes, that can be used too

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Thank you very much :) I think i will trey use biopython to read in the existing gbk and edit it with new annotations

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14 months ago
Mensur Dlakic ★ 15k

If you prefer to do this using GUI, I will suggest an old program called GENtle. That wouldn't be a good solution for hundreds or thousands of genes, but it will probably work for viral genomes. You can import your GenBank file, and then double-click on each gene in the map and update its record. Finally, export as GenBank and that should be it.

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