- Search for TFs
- Search for Genes
- Search for Associations
Support & suggestions:
This utility searches for the motifs in a given list in the motifs from the other list. It allows for the comparison of new DNA motifs (for instance, those over-represented in the promoter regions of co-regulated genes) with DNA motifs which are not described in the YEASTRACT database (for instance, DNA motifs found to be conserved in the promoter regions of closely related yeast species but not associated with a specific TF).
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The search can be performed to determine whether the list 1 motifs are
contained in the list 2 motifs, or vice versa. The user can allow for
up to two substitutions.
The output is a set of pairs of motifs, one from each list, that are found to match each other, the position at which the match was found and the strand (forward or reverse).Back to top
Simple nucleotide sequences are strings that
consist exclusively of the four characters that represent the DNA
A, T, G and C. A search for a given simple nucleotide sequence only
sequences that match the query string exactly.
Standard IUPAC Nucleotide code is used to describe ambiguous sites in a given DNA sequence motif, where a single character may represent more than one nucleotide. The code is shown in the table below.
Table adapted from .Back to top
A regular expression is a pattern containing characters and syntactic elements that matches a set of strings. The regular expression characters permitted in the searches for DNA motifs are those included in the IUPAC nucleotide code as well as the following syntactic element:
 – Matches one of the characters contained in the brackets.Back to top
 Biochem J. 1985 July 15; 229(2): 281–286. (PubMed)
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