[BiO BB] Promoter Analysis

Harry Mangalam hjm at tacgi.com
Mon Jul 21 18:28:47 EDT 2003

sounds like tacg might be of use.

it can take an arbitrary number of patterns formatted as IUPAC patterns, regular 
expressions, or transfac matrices (altho not mixed) and search large numbers of 
input sequences.  Especially useful for your search, it can also search for 
pattern /sets/ that you define as useful or interesting - ie: if A, B, C, D, E, 
and F represent IUPAC patterns such as gyrnngttgtynnng, you could search for


Look at tacg.sf.net and if it looks interesting, let me know and I'll send you 
version 4 which is just about finished.


Jan Torleif Pedersen wrote:
> Greetings,
> I hope not everybody is away on vacation !
> We are running some custom spotted microarrays in our microbiology
> department and
> I would like to run a promoter analysis on all the genes on the chip. To
> that end I would need
> a promoter analysis program that I can run in batch-mode and a set of
> promoter patterns.
> Could someone advice on the program and library of choice. 
> 		Many Regards    -- Jan
> Dr. Jan Torleif Pedersen
> Section head, Bioinformatics
> Department of Molecular Genetics
> H. Lundbeck A/S
> Ottiliavej 9, 2500 DK-Valby
> Denmark
> phone: +45 36 43 28 87
> FAX: 36438271
> email: jatp at lundbeck.com
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hjm at tacgi.com
             <<plain text preferred>>
         Go Dennis! http://www.kucinich.us

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