[BiO BB] predicting promoter regions

Maximilian Haeussler maximilianh at gmail.com
Sun Oct 29 18:08:31 EST 2006

Hi Rich,

I don't think that you have a good understanding of the difference
between predicting enhancers/promoters on the one and analysing their
content on the other hand. transfac isn't a software and cannot
predict promoters.

In short:

a) promotor are assumed to be located to the start of transcription
you can use software like FIE or dragon promoter prediction for these.

b) enhancers are the other type of cis-regulatory elements. you can
use software like phastCons or RP on UCSC (current version is called
ESPERR) to predict them. This assumes multiple alignments available
for your sequences

c) once you have them identified you can apply transfac scanners like
those from toucan for them. But you should really know what you are
doing here. Try a random sequence to get an impression that toucan can
predict anything everywhere.

You can have a look at my masters at
http://www.stud.uni-potsdam.de/masters or at my transcriptional
regulation wiki www.stud.uni-potsdam.de/wiki. for an introduction to
promoter prediction / analysis you can try the tutorials at
genomatix.de.  Any other introductions available that anyone knows of?


On 20/10/06, rich <rich at thevillas.eclipse.co.uk> wrote:
> Hi,
> can anybody recommend any tools for predicting promoter/regulatory regions?
> I believe TRANSFAC is one? Any others that people would recommend?
> Cheers
> Rich
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Maximilian Haeussler,
skype: maximilianhaeussler

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