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DescriptionCONREAL web server allows identification of transcription factor binding sites (TFBS) that are conserved between two [orthologous promoter] sequences. The predictions can be performed by four different methods (CONREAL-, LAGAN-, MAVID- and BLASTZ-based) and results can be compared to each other.
Input sequencesProvide a pair of orthologous sequences in FASTA format or, alternatively, type in ENSEMBL gene ID or keyword to retrieve sequences of interest from ENSEMBL database.
Search parametersThere are 3 parameters that can be set:
Interpretation of resultsOutput consists of a graph, alignment and a table with predicted TFBSs. A graph shows aligned positions in the orthologous sequences and the density of predicted TFBS, facilitating general assessment of predictions and identification of TFBS "hot spots". A pairwise alignment of sequences provides single nucleotide resolution information, whereas a table with predicted conserved TFBS, sorted by position in the alignment and linked to JASPAR and TRANSFAC databases, supplies more detailed information on the transcription factors. Furthermore, when multiple algorithms were selected for analysis, the overlap between predictions by the different algorithms is shown for every TFBS thus providing a means for evaluation of prediction reliability.
CitationBerezikov E, Guryev V, Plasterk R.H., Cuppen E. (2004) CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Res., 14, 170-178.
Berezikov E, Guryev V, Cuppen E. (2005) CONREAL Web Server: Identification and Visualization of Conserved Transcription Factor Binding Sites. In preparation.