[Bio-software] Re: Promotor analysis software

darked via bio-soft%40net.bio.net (by darek.kedra from gmail.com)
Mon Oct 22 11:10:12 EST 2007

On Oct 20, 10:57 pm, "Aparecida Fontes" <fonte... from pegasus.fmrp.usp.br>
> Dear Prof ,
> I´m a professor from Brazil.
> I have seen you have a sofware for promoter analysis.
> I´m writing a paper about stem cells and I analyzed by real time PCR the difference of level expression among 10 genes in 6 cell types.
> Our analysis suggests that there are relations among some genes.
> So, I would like to find the promoter region of these 10 genes and investigate if there is common transcription factor among them.
> Could you help me?
> Thanks a lot
> Aparecida
> Aparecida Maria Fontes, PhD
> Pesquisadora Cientifico Tecnologico II
> Centro Regional de Hemoterapia- HC-FMRP/USP
> Centro de TErapia Celular
> R. Tenente Catao Roxo, 2501
> 14051-150
> Ribeirao PReto, SP Brazil
> Phone 55-16-21019371


I guess you are investigating human sequences?
1. try to extract upstream sequences using i.e http://www.biomart.org/
2. for a set of sequences yo may search using GLAM http://zlab.bu.edu/glam/
see alos other tools from http://sullivan.bu.edu/zlab/gene.shtml site
3. if yo want to do de novo motif discovery there are a couple of
programs, such as MEME (http://meme.sdsc.edu/meme/meme.html) and
NestedMICA http://www.sanger.ac.uk/Software/analysis/nmica/

Hope it helps.


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