[mira_talk] Re: Plasmid DNA
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 28 Jun 2013 11:40:28 -0400
It probably cannot happen.
Mira quits at heavy repeats, and most of our contigs have rRNA, insertion
sequences, or other repeats at their termini. Given an rRNA operon or any
other repeat in an inconvenient orientation, it will look like a circular
contig. Mira does not even circularize whole singular bacterial chromosomes.
You have to trim the ends and do it yourself.
John
On 2013-06-28, at 11:34 AM, Adrian Pelin <apelin20@xxxxxxxxx> wrote:
> Talking about both. I am aware of your steategy, which requires individual
> contig examination, so its lenghthy.
>
>
> Any way mira can tell us putative circular contigs?
>
> Sincerely,
> Adrian
>
> On 2013-06-28, at 11:15 AM, Hanquan Liang <hliang@xxxxxxx> wrote:
>
>> I think not sure if Adrian is talking about plastids in eukaryotes, or
>> plasmids in bacteria?
>>
>> Plastids usually have multiple copies, so they have higher coverage than
>> average level.
>> Also, if you have paired-end reads, map them to the contigs, and you should
>> see pairs connecting 5' and 3' end of the contig.
>>
>> Hanquan
>>
>>
>> On Fri, Jun 28, 2013 at 3:01 AM, Tibor Nagy <black00710@xxxxxxxxx> wrote:
>> Hello,
>>
>> When I had a problem like this, I collected a large number of plasmid
>> sequences and I made a blast search against it. This is the most simple
>> approach, but it is working.
>>
>> Tibor
>>
>>
>> On Fri, Jun 28, 2013 at 3:06 AM, Adrian Pelin <apelin20@xxxxxxxxx> wrote:
>> Hello,
>>
>> I was wondering, right now I am working on eukaryotic stuff, and I am
>> assembling nuclear genomes. But I bet, that sometimes presence of plasmid is
>> overlooked and never discovered because there is no clear way to do see if
>> you have a plasmid in your sequence.
>>
>> The assembler however, should know, if it sees that upon extending the
>> contigs 3' it hits the 5'
>>
>> How would we investigate such cases for the putative presence of plasmids?
>>
>> Adrian
>>
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