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DISCOVERER

Regulatory Associations:
- Search for TFs
- Search for Genes
- Search for Associations

Group genes:
- Group by TF
- Group by GO

Pattern Matching:
- Search by DNA Motif
- Find TF Binding Site(s)
- Search Motifs on Motifs

Utilities:
- ORF List ⇔ Gene List
- IUPAC Code Generation
Generate Regulation Matrix

Retrieve:
- TF-Consensus List
- Evidence Code List
- Upstream Sequence
- Flat files

About Yeastract:
- Contact Us
- Cite YEASTRACT
- Acknowledgments
- Credits


Support & suggestions:

KDBIO/INESC-ID IST

Search by DNA Motif in the Promoter Regions of Genes - Help

BSRG/IST

Index

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



1. Summary


This query allows the user to search for one or more DNA motifs within yeast promoter regions (either all or selected ones). The query string may be a simple nucleotide sequence, a sequence containing IUPAC nucleotide code or even a sequence containing regular expression elements. The forward and reverse strands of the promoters are searched for the input motifs.


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2. Examples


Pattern

Matches

TATATAAG TATATAAG
TATAWAAM TATAAAAC, TATAAAAA, TATATAAC, TATAAAAA
TATA[GC]AA[AT] TATAGAAT, TATAGAAA, TATACAAT, TATACAAA

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3. Input

This query requires a list of patterns to be searched for and, optionally, a list of genes. The patterns to be searched for must be at least four bases long.

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4. Options


If both a list of patterns and genes are introduced, the default option is to search for the patterns in the promoter regions of those genes. If, however, the user selects the Check for all Genes option, then the promoter regions of all genes in the database are searched for the input patterns. This option is aimed at the identification of genes under the same regulatory signaling. It is also possible to allow for one or two nucleotide substitutions in the input pattern, by selecting the corresponding value in the box labelled Substitutions.

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5. Output


The search returns a list of genes in whose promoters the patterns were found, including the number of occurences in each promoter. By clicking in the entries in the column named View, a view of the forward and reverse strands of the corresponding promoter, highlighted where it matched the query, is afforded. The patterns that matched the promoter sequences and their locations in the promoters are also displayed.

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6. 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.

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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

Table adapted from [1].

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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.

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7. References


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


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