CONREAL web server: identification and visualization of conserved transcription factor binding sites
Open Access
- 1 July 2005
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 33 (Web Server) , W447-W450
- https://doi.org/10.1093/nar/gki378
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.Keywords
This publication has 10 references indexed in Scilit:
- Ensembl 2005Nucleic Acids Research, 2004
- rVISTA 2.0: evolutionary analysis of transcription factor binding sitesNucleic Acids Research, 2004
- ConSite: web-based prediction of regulatory elements using cross-species comparisonNucleic Acids Research, 2004
- MAVID: Constrained Ancestral Alignment of Multiple SequencesGenome Research, 2004
- JASPAR: an open-access database for eukaryotic transcription factor binding profilesNucleic Acids Research, 2004
- CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic FootprintingGenome Research, 2003
- LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNAGenome Research, 2003
- TRANSFAC(R): transcriptional regulation, from patterns to profilesNucleic Acids Research, 2003
- Human–Mouse Alignments with BLASTZGenome Research, 2002
- AVID: A Global Alignment ProgramGenome Research, 2002