Description
CONREAL 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 sequences
Provide 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 parameters
There are 3 parameters that can be set:
- PWM threshold - minimum relative score of a TFBS hit to be considered in the analysis, in percentages.
- Length of flanks - number of bases flanking a TFBS to include for calculating homology.
- Threshold for homology - minimal percentage of homology between two TFBS sites, including flanking sequences.
In addition, it is possible to specify sources of PWMs and alignment methods to use (CONREAL, LAGAN, MAVID or BLASTZ).
Currently, CONREAL web server uses 81 vertebrate matrices form JASPAR database and
546 matrices from TRANSFAC database (v.8.4).
Interpretation of results
Output 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.
Citation
Berezikov 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.
Contact
Eigene Berezikov
|
