[BiO BB] Promoter Analysis
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
(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.
Jan Torleif Pedersen wrote:
> 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
> phone: +45 36 43 28 87
> FAX: 36438271
> email: jatp at lundbeck.com
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
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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