Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2003 Jul 1;31(13):3666-8.
doi: 10.1093/nar/gkg540.

Cluster-Buster: Finding dense clusters of motifs in DNA sequences

Martin C Frith  1 , Michael C Li, Zhiping Weng
Affiliations

Cluster-Buster: Finding dense clusters of motifs in DNA sequences

Martin C Frith et al. Nucleic Acids Res. .

Abstract

The signals that determine activation and repression of specific genes in response to appropriate stimuli are one of the most important, but least understood, types of information encoded in genomic DNA. The nucleotide sequence patterns, or motifs, preferentially bound by various transcription factors have been collected in databases. However, these motifs appear to be individually too short and degenerate to enable detection of functional enhancer and silencer elements within a large genome. Several groups have proposed that dense clusters of motifs may diagnose regulatory regions more accurately. Cluster-Buster is the third incarnation of our software for finding clusters of pre-specified motifs in DNA sequences. We offer a Cluster-Buster web server at http://zlab.bu.edu/cluster-buster/.

PubMed Disclaimer

Figures

Figure 1
Figure 1
(A) Overview of motif clusters and protein-coding regions in GenBank sequence AY007685. (B) Detailed view of the second strongest motif cluster.
Figure 1
Figure 1
(A) Overview of motif clusters and protein-coding regions in GenBank sequence AY007685. (B) Detailed view of the second strongest motif cluster.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Arnone M.I. and Davidson,E.H. (1997) The hardwiring of development: organization and function of genomic regulatory systems. Development, 124, 1851–1864. - PubMed
    1. Berman B.P., Nibu,Y., Pfeiffer,B.D., Tomancak,P., Celniker,S.E., Levine,M., Rubin,G.M. and Eisen,M.B. (2002) Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl Acad. Sci. USA, 99, 757–762. - PMC - PubMed
    1. Prestridge D.S. (1995) Predicting Pol II promoter sequences using transcription factor binding sites. J. Mol. Biol., 249, 923–932. - PubMed
    1. Kondrakhin Y.V., Kel,A.E., Kolchanov,N.A., Romashchenko,A.G. and Milanesi,L. (1995) Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci., 11, 477–488. - PubMed
    1. Crowley E.M., Roeder,K. and Bina,M. (1997) A statistical model for locating regulatory regions in genomic DNA. J. Mol. Biol., 268, 8–14. - PubMed

Publication types

Substances