Hi!
I have a complete bacterial genome assembled in 1 contig. I have manually made the sequence to start with the first nucleotide of the DnaA gene, and uploaded it on RAST for annotations. But after completion of annotation, it is giving a warning of convergent contig.
Can you please help me resolve this error.
Thanks!
Probably the warning looks as 'convergent overlap'.
See the RAST Quality report below:
http://www.theseed.org/wiki/RAST_Quality_Report
Go to Overlaps there. This is not fatal, first of all.
"the overlap exceeds the (default) threshold of 50 bp.
Such overlaps are considered "Warning" conditions, not fatal.
Overlaps by less than threshold are not reported."
So check your contig and remove a small part of it.
On the other hand my advice would be to start bacterial sequence
150-200 nucleotides before DnaA - gene start. Otherwise you may loose
some specific binding sites.
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version 2.3.6
Thank you for your reply.
How should I check my contig for overlaps? and should I randomly take 150 or 200 nucleotides before DnaA gene start?
I think this overlap can be found by muscle-alignment. I would divide a contig into several parts and align each one of the pieces with initial contig. If one alignment is divided into several separate fragments, this is a sign of potential overlap. Let's suppose, you have 5 parts. First part should align with the first part of contig only, and not with second, third, forth and fifth ones.
As to DnaA - see the post
A: Position 1 in closed circular genome.
We took a fragment between dnaA-gene and rpmH-gene and started a bacterial DNA somewhere in between, approximately in the middle of that fragment. Try to find repeats that might bind DnaA in the region between DnaA-gene and rpmH as well, and include all of them into this upatream fragment.