FOOTPRINTER
From Indipedia: India's Wikipedia at OSDD
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.
One of the current challenges facing biologists is the discovery of novel functional elements in non-coding genomic sequence.
With the rapidly increasing number of genomes being sequenced, a comparative genomics approach called ‘phylogenetic footprinting’ has become a favored method for such discovery. This note focuses on the discovery of novel regulatory elements. The idea underlying phylogenetic footprinting is that selective pressure causes regulatory elements to evolve at a slower rate than the non-functional surrounding sequence. Therefore the best conserved motifs in a collection of homologous regulatory regions are excellent candidates as regulatory elements. The traditional method that has been used for phylogenetic footprinting is to construct a global multiple alignment of the homologous regulatory sequences and then identify well conserved aligned regions However, this approach fails if the regulatory regions considered are too diverged to be accurately aligned. we described an algorithm designed specifically for phylogenetic footprinting. Instead of relying on multiple alignment, we attack the problem with a motif discovery approach. Given a set of homologous input sequences and the phylogenetic tree T relating them, the algorithm identifies every set of kmers, one from each input sequence, that have parsimony score at most d with respect to T, where k and d are parameters specified by the user. (The parsimony score is the minimum number of nucleotide substitutions along the branches of T that explain the set of identified kmers.) This algorithm has been implemented in a program called FootPrinter.
The simple web form asks the user to supply the homologous input sequences in Fasta format. The first word of each sequence annotation line following ‘>’ must correspond to the name of a species in the phylogenetic tree. The user also supplies the phylogenetic tree relating the sequences, although if the tree is absent FootPrinter will use a default species tree containing many of the most commonly used eukaryotic species. If the user chooses to enter a phylogeny, it is given in the usual bracket form.
FootPrinter's results are made available in three formats, HTML, Postscript and plain text. The HTML format is assumed in what follows, as it provides the most information in a graphical, interactive form.
[edit] Protocol
It is important when using this technique to decide which genome your sequence should be aligned to. More divergent species will have less sequence homology between orthologous genes. Therefore, the key is to pick species that are related enough to detect homology, but divergent enough to maximize non-alignment “noise”. Step wise approach to Phylogenetic footprinting consists of :
- One should decide on the gene of interest.
- Carefully choose species with orthologous genes.
- Decide on the length of the upstream or maybe downstream region to be looked at.
- Align the sequences.
- Look for conserved regions and analyse them.
