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Old 04-03-2012, 10:20 AM   #1
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Location: East coast

Join Date: Jul 2010
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Default How to circularize plasmid assembly

My assembly resulted in a single contig, which is linear. How do I check where is the complimentary sequences on the ends so that I could circularize the plasmid? Is there a tool that can do that easily?

The thing is I have ran several assemblies and got several one-contigs, but they differ slightly in size, so I expect the difference to be in tails. I have aligned the contigs in Mauve and see that 95% of contigs overlap, but I still cannot figure out where to trim the tails so that I could circularize the plasmid.

I would appreciate any help and pointers.
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Old 04-04-2012, 02:58 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

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You can use tools like mummerplot to compare the contig to itself, and thus deduce the circle.

Since (AFAIK) no read mappers support a circular reference, you can check the circle like so: Once you've made the circle, try mapping the reads to it. Then shift the origin (say half way along) and repeat this mapping. Both times you should get nice uniform coverage. Or, take two copies of the circle as a single long reference, and map the reads to that - again you're looking for nice uniform coverage.
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Old 04-04-2012, 07:14 AM   #3
Location: St. Louis, MO

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What you could do is chop your sequence in half (at what ever break point is appropriate) and then run it through minimus2 or another OLC. If you get one contig back, you now have a perfect linear representation of a circular plasmid. Now you know that the ends can be connected bluntly.
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