[BiO BB] Promoter Analysis

[Harry Mangalam]

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

(A AND ((B XOR C) OR (D AND F)) NOT (E OR A))

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.

harry

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
> 
> _______________________________________________
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> 

-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hjm at tacgi.com
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