[mira_talk] Re: Plasmid DNA
- From: Hanquan Liang <hliang@xxxxxxx>
- To: mira_talk <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 28 Jun 2013 10:15:19 -0500
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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