Footprinter

FootPrinter: a program designed for phylogenetic footprinting. Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the best conserved motifs in those homologous regions. This note describes web software that has been designed specifically for this purpose, making use of the phylogenetic relationships among the homologous sequences in order to make more accurate predictions. The software is called FootPrinter and is available at http://bio.cs.washington.edu/software.html.


References in zbMATH (referenced in 10 articles )

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  1. Retzlaff, Nancy; Stadler, Peter F.: Partially local multi-way alignments (2018)
  2. Mosig, Axel; Bıyıkoğlu, Türker; Prohaska, Sonja J.; Stadler, Peter F.: Discovering cis-regulatory modules by optimizing barbecues (2009)
  3. Nguyen, Tung T.; Androulakis, Ioannis P.: Recent advances in the computational discovery of transcription factor binding sites (2009)
  4. Sun, Yi; González Castellano, Cristina; Robinson, Mark; Adams, Rod; Rust, Alistair G.; Davey, Neil: Using pre & post-processing methods to improve binding site predictions (2009)
  5. Sun, Yi; Robinson, Mark; Adams, Rod; te Boekhorst, Rene; Rust, Alistair G.; Davey, Neil: Integrating genomic binding site predictions using real-valued meta classifiers (2009) ioport
  6. Janky, Rekin’s; Van Helden, Jacques: Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution (2008) ioport
  7. Robinson, Mark; Castellano, Cristina González; Rezwan, Faisal; Adams, Rod; Davey, Neil; Rust, Alastair; Sun, Yi: Combining experts in order to identify binding sites in yeast and mouse genomic data (2008)
  8. Levitsky, Victor G.; Ignatieva, Elena V.; Ananko, Elena A.; Turnaev, Igor I.; Merkulova, Tatyana I.; Kolchanov, Nikolay A.; Hodgman, T. C.: Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions (2007) ioport
  9. Sun, Yi; Robinson, Mark; Adams, Rod; Kaye, Paul; Rust, Alistair; Davey, Neil: Integrating binding site predictions using non-linear classification methods (2005)
  10. Blanchette, Mathieu; Tompa, Martin: Footprinter: a program designed for phylogenetic footprinting. (2003) ioport