FootPrinter3 -- phylogenetic footprinting in partially alignable sequences
What you can do:
Discover regulatory elements in a set of homologous regulatory regions.
Highlights:
- FootPrinter3 is a web server for predicting transcription factor binding sites by using phylogenetic footprinting.
- It integrates these two approaches, making use of local multiple sequence alignment blocks when those are available and reliable, but also allowing finding motifs in unalignable regions.
- The result is a set of predictions that joins the advantages of alignment-based methods (good specificity) to those of motif-based methods (good sensitivity, even in the presence of highly diverged species).
- FootPrinter3 is thus a tool of choice to exploit the wealth of vertebrate genomes being sequenced, as it allows taking full advantage of the sequences of highly diverged species (e.g. chicken, zebrafish), as well as those of more closely related species (e.g. mammals).
Keywords:
- phylogenetic footprinting tool
- transcription factor binding site analysis tool
- DNA-binding sites prediction tool
- promoter analysis tool
- transcription factor binding sites
- cis-elements prediction tool
- regulatory element prediction tool
- promoter element prediction tool
Literature & Tutorials:
PubMed Link: FootPrinter -- a program designed for phylogenetic footprinting
PubMed Link of 2006 update: FootPrinter3: phylogenetic footprinting in partially alignable sequences
PubMed Link of 2006 update: FootPrinter3: phylogenetic footprinting in partially alignable sequences
This record last updated: 08-03-2006