Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W447-50.

CONREAL web server: identification and visualization of conserved transcription factor binding sites.

Source

Hubrecht Laboratory, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands. berezikov@niob.knaw.nl

Abstract

The use of orthologous sequences and phylogenetic footprinting approaches have become popular for the recognition of conserved and potentially functional sequences. Several algorithms have been developed for the identification of conserved transcription factor binding sites (TFBSs), which are characterized by their relatively short and degenerative recognition sequences. The CONREAL (conserved regulatory elements anchored alignment) web server provides a versatile interface to CONREAL-, LAGAN-, BLASTZ- and AVID-based predictions of conserved TFBSs in orthologous promoters. Comparative analysis using different algorithms can be started by keyword without any prior sequence retrieval. The interface is available at http://conreal.niob.knaw.nl.

PMID:: 15980509; [PubMed - indexed for MEDLINE]
PMCID:: PMC1160139

Free PMC Article

Images from this publication.See all images (2) Free text

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

Transcription Factors

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Molecular Biology Databases

CONREAL - Bioinformatics.ca Links Directory

Supplemental Content

Save items

Related citations in PubMed

CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. [Genome Res. 2004]
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting.
Berezikov E, Guryev V, Plasterk RH, Cuppen E. Genome Res. 2004 Jan; 14(1):170-8. Epub 2003 Dec 12.
Exploring conservation of transcription factor binding sites with CONREAL. [Methods Mol Biol. 2007]
Exploring conservation of transcription factor binding sites with CONREAL.
Berezikov E, Guryev V, Cuppen E. Methods Mol Biol. 2007; 395:437-48.
ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species. [Nucleic Acids Res. 2008]
ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species.
Hooghe B, Hulpiau P, van Roy F, De Bleser P. Nucleic Acids Res. 2008 Jul 1; 36(Web Server issue):W128-32. Epub 2008 May 3.
Review Tumor growth simulation and visualization: a review and a Web based paradigm. [Stud Health Technol Inform. 2000]
Review Tumor growth simulation and visualization: a review and a Web based paradigm.
Stamatakos GS, Uzunoglu NK, Delibasis K, Mouravliansky N, Marsh A, Makropoulou M. Stud Health Technol Inform. 2000; 79:255-74.
Review Promoter analysis. [Ernst Schering Res Found Works...]
Review Promoter analysis.
Werner T. Ernst Schering Res Found Workshop. 2002; (38):65-82.

See reviews... See all...

Cited by 10 PubMed Central articles

ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. [Bioinformatics. 2012]
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites.
González S, Montserrat-Sentís B, Sánchez F, Puiggròs M, Blanco E, Ramirez A, Torrents D. Bioinformatics. 2012 Mar 15; 28(6):763-70. Epub 2012 Jan 16.
Identification of cis-regulatory elements in the mammalian genome: the cREMaG database. [PLoS One. 2010]
Identification of cis-regulatory elements in the mammalian genome: the cREMaG database.
Piechota M, Korostynski M, Przewlocki R. PLoS One. 2010 Aug 31; 5(8):e12465. Epub 2010 Aug 31.
Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach. [Mamm Genome. 2010]
Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach.
Rodríguez-Flores JL, Zhang K, Kang SW, Wen G, Ghosh S, Friese RS, Mahata SK, Subramaniam S, Hamilton BA, O'Connor DT. Mamm Genome. 2010 Apr; 21(3-4):195-204. Epub 2010 Mar 5.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

CONREAL web server: identification and visualization of conserved transcription ...
CONREAL web server: identification and visualization of conserved transcription factor binding sites.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W447-50.

PubMed
WordSpy: identifying transcription factor binding motifs by building a dictionar...
WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W412-6.

PubMed
enoLOGOS: a versatile web tool for energy normalized sequence logos.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W389-92.

PubMed
Protein structure prediction servers at University College London.
Protein structure prediction servers at University College London.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W36-8.

PubMed
FFAS03: a server for profile--profile sequence alignments.
FFAS03: a server for profile--profile sequence alignments.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W284-8.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: