FOOTER -- a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
What you can do:
Analyze homologous mammalian promoter sequences in order to identify transcriptional DNA regulatory signals.
Highlights:
- FOOTER uses prior knowledge about the binding site preferences of the transcription factors (TFs) in the form of position-specific scoring matrices (PSSMs).
- The PSSM models are generated from known mammalian binding sites from the TRANSFAC database.
- In a test set of 72 confirmed binding sites (most of them not present in TRANSFAC) of 19 TFs, it exhibited 83% sensitivity and 72% specificity.
Keywords:
- transcription factor binding site prediction tool
- transcription factor binding site analysis tool
- DNA-binding sites prediction tool
- cis-elements prediction tool
- cis-regulatory elements prediction tool
- promoter analysis tool
- promoter elements prediction tool
- transcription factors
- response elements
- cis-elements
- cis-regulatory modules analysis tool
- regulatory motifs
- regulatory motif discovery tool
- mammalian promoters
- mammalian regulatory motifs
- mammalian cis-regulatory elements
- phylogenetic footprinting
- phylogeny
Literature & Tutorials:
This record last updated: 11-21-2005