This Web site is devoted to finding binding sites for regulatory proteins in DNA and RNA sequences. Currently it contains a program to find the sites, and some examples of the sites the program has found.
Improbizer - A program that slowly crawls through DNA or RNA sequence looking for consensus motifs that happen improbably often.
Motif Matcher - See where given motifs occur in your sample.
Yeast Promoters - A series of studies on yeast promoters.
Ribosomal Protein Promoters 1 - Motifs found using a simple Markov 0 background model and up to two occurrences of each motif on a collection of 103 sequences of 500 bp each taken from the region upstream of translation start on genes which show the expression pattern of ribosomal proteins.
Ribosomal Protein Promoters 2 - Motifs found using a Markov 1 background model based on several thousand yeast upstream regions on same data as above.
C. Elegans Introns - Searches for motifs in C. elegans introns.
Short Introns Before Skipped Exons 1 - Foreground data is the introns 350 bp or shorter before occassionally skipped exons. Looking for 2 occurrences of each motif. (Control).
Short Before Skipped Exons 1 - Foreground data is 50 bp of intron before an exon that is sometimes spliced in and sometimes not. Background is Markov 1 model of 3' ends of 28,000 C. elegans introns. Improbizer was set to look for up to two occurrences of each motif.
Short Before Skipped Exons 2 - Same as above but only looking for one occurence of each motif per sequence.