PUBLICATION
FootPrinter3: phylogenetic footprinting in partially alignable sequences
- Authors
- Fang, F., and Blanchette, M.
- ID
- ZDB-PUB-060724-16
- Date
- 2006
- Source
- Nucleic acids research 34: W617-620 (Other)
- Registered Authors
- Fang, Fang
- Keywords
- none
- MeSH Terms
-
- Animals
- Binding Sites
- DNA Footprinting/methods*
- Genomics/methods*
- Internet
- Phylogeny
- Promoter Regions, Genetic*
- Sequence Alignment/methods*
- Software*
- Transcription Factors/metabolism*
- User-Computer Interface
- PubMed
- 16845084 Full text @ Nucleic Acids Res.
Citation
Fang, F., and Blanchette, M. (2006) FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic acids research. 34:W617-620.
Abstract
FootPrinter3 is a web server for predicting transcription factor binding sites by using phylogenetic footprinting. Until now, phylogenetic footprinting approaches have been based either on multiple alignment analysis (e.g. PhyloVista, PhastCons), or on motif-discovery algorithms (e.g. FootPrinter2). FootPrinter3 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). The FootPrinter3 web server is available at: http://www.mcb.mcgill.ca/~blanchem/FootPrinter3.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping