[mira_talk] Re: 500Mb assembly
- From: Brian Forde <bforde@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 11 Dec 2009 11:24:14 +0000
maybe that is the repeat sequence which is than repeated in
tandem/interspaced X times
On Fri, Dec 11, 2009 at 10:12 AM, Filip Van Nieuwerburgh <
Filip.VanNieuwerburgh@xxxxxxxx> wrote:
> Thanks Björn. I think you are right. The Apis melliferas genome is far from
> finished. Probably the bigger repeats are not in the NCBI genome sequence.
>
> Kind regards,
> Filip
>
>
> -----Original Message-----
> From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:
> mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Björn Nystedt
> Sent: vrijdag 11 december 2009 10:44
> To: mira_talk@xxxxxxxxxxxxx
> Subject: [mira_talk] Re: 500Mb assembly
>
> Hi Filip,
> the answer might perhaps be simple: the published sequence could well be
> what is left after filtering away or collapsing all repeats larger than 2kb.
> Then only 2kb repeats remains...
>
> B
>
>
>
> On Fri, 11 Dec 2009 09:36:30 +0100
> "Filip Van Nieuwerburgh" <Filip.VanNieuwerburgh@xxxxxxxx> wrote:
>
> > The biggest IDENTICAL repeat was 2205bp. To find this, I used the
> > programs UGENE and findpat. Both programs gave exactly the same results.
> > I must say that I am also skeptical about this result. Maybe I should
> > run these programs on an validation dataset. Suggestions are welcome.
> >
> > Kind regards,
> > Filip
> >
> > -----Original Message-----
> > From: mira_talk-bounce@xxxxxxxxxxxxx
> > [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Bastien Chevreux
> > Sent: donderdag 10 december 2009 19:51
> > To: mira_talk@xxxxxxxxxxxxx
> > Subject: [mira_talk] Re: 500Mb assembly
> >
> > On Donnerstag 10 Dezember 2009 Filip Van Nieuwerburgh wrote:
> > > I checked the repeats in the most closely related genome (honey bee).
> > > The biggest repeat was around 2000bp.
> >
> > I'm a bit sceptical here. Even bacteria have repeats larger than that
> > and many
> > of them you don't get assembled completely with only a 3kb library.
> >
> > You've got a higher eukaryote ... how did you get to 2k as maximum
> > repeat
> > size?
> >
> > Regards,
> > Bastien
> >
> > --
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>
> --
> ====================================
> Björn Nystedt, PhD
> Molecular Evolution
> EBC, Uppsala University
> Norbyv. 18C, 752 36 Uppsala
> Sweden
> phone: +46 (0)18-471 45 88
> email: Bjorn.Nystedt@xxxxxxxxx
> ====================================
>
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