Index

1. Summary
2. Input
3. Options
4. Output
5. Notes
   1. Simple Nucleotide Sequences
   2. IUPAC Nucleotide Code
   3. Regular Expressions
6. References

---

1. Summary

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).

Back to top

---

2. Input

The required input are two lists of DNA motifs. These motifs can be simple nucleotide sequences, contain IUPAC nucleotide code or even contain regular expression elements.

Back to top

---

3. Options

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.
Furthermore, the user may restrict its search to the regulatory associations identified based on direct or indirect evidences. Direct Evidence was considered to be provided through experiments such as Chromatine ImmunoPrecipitation (ChIP), ChIP-on-chip and Electrophoretic Mobility Shift Assay (EMSA), that prove the direct binding of the TF to the target gene's promoter region, or such as the analysis of the effect on target-gene expression of the site-directed mutation of the TF binding site in its promoter region, which strongly suggests that the TF interacts with that specific target promoter. The classification Indirect Evidence was attributed to experiments such as the comparative analysis of gene expression changes occurring in response to the deletion, mutation or over-expression of a given TF. The complete enumeration of the experimental approaches considered to provide direct or indirect evidences is provided in Table Evidence code list.

Back to top

---

4. Output

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

---

5. Notes

Simple Nucleotide Sequences

Simple nucleotide sequences are strings that consist exclusively of the four characters that represent the DNA nucleotides: A, T, G and C. A search for a given simple nucleotide sequence only returns sequences that match the query string exactly.

Back to top

IUPAC Nucleotide Code

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.

IUPAC Code	Meaning	Origin of Description
G	G	Guanine
A	A	Adenine
T	T	Thymine
C	C	Cytosine
R	G or A	puRine
Y	T or C	pYrimidine
M	A or C	aMino
K	G or T	Ketone
S	G or C	Strong interaction
W	A or T	Weak interaction
H	A or C or T	not-G, H follows G in the alphabet
B	G or T or C	not-A, B follows A in the alphabet
V	G or C or A	not-T (not-U), V follows U in the alphabet
D	G or A or T	not-C, D follows C in the alphabet
N	G or A or T or C	aNy

Back to top

Regular Expressions

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

---

6. References

[1] Biochem J. 1985 July 15; 229(2): 281–286. (PubMed)

Back to top