[mira_talk] Re: 500Mb assembly
- From: "Filip Van Nieuwerburgh" <Filip.VanNieuwerburgh@xxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 11 Dec 2009 11:12:44 +0100
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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