[mira_talk] Re: 500Mb assembly
- From: "Filip Van Nieuwerburgh" <Filip.VanNieuwerburgh@xxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 11 Dec 2009 09:36:30 +0100
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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