How do you add an ORF that overlaps the two regions where a circular genome is cut in Genbank?
Entering edit mode
12 months ago
Chvatil ▴ 130

Dear Biostars community,

I had a question regarding the BankIt (Genbank) submission for circularized genomes.

Let's say I have a circularized genome from 1 to 100000 bp.

And I also have a predicted ORF from 99000 to 20 (so where the genome is split in two).

How Can I code this information to get only one ORF from 99000 to 20 (1020bp) and not to 20 to 99000 (98980bp) ?

All the best,

Here is the way I code the feature BankIt table : 20 99000 gene locus_tag Chr1 CDS Product 20 99000 nan product hypothetical protein transl_table 1

genbank • 415 views
Entering edit mode
12 months ago
Chvatil ▴ 130

In case one day someone asks himself how to do that, here is the answer :

You may enter two coding regions for the CDS with the coordinates as follows:

99000   100000   CDS
1    20
               codon_start   1
               product     xxxxxxxx

You will get the joined CDS like this:

CDS             join(99000..100000,1..20)

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