TOUCAN is a handy application that can be used as a workbench for regulatory sequence analysis on metazoan genomes.
TOUCAN can be used for comparative genomics, detection of cis-regulatory modules and the detection of signification transcription factor binding sites.
TOUCAN is written using Java and is available for all major platforms, including Mac OS X, Windows and Linux.
Here are some key features of "TOUCAN":
· Retrieve (upstream) sequences and annotation from Ensembl and EMBL automatically
· Retrieve (upstream) sequences of one or more ortologous genes automatically
· Visualize a sequence set with all annotated features
· Add annotation in GFF format
· CpG island annotation
· Align large genomic regions with various specialized algorithms like AVID, LAGAN, or BLASTZ
· Easily select potentially interesting regulatory regions, like conserved non-coding sequences (CNS) and proximal promoters
· Predict instances of known transcription factors using the MotifScanner algorithm (with higher-order background models), with libraries of position weight matrices (e.g., TRANSFAC, JASPAR)
· Detect over-represented instances of these factors using a binomial distribution model
· Detect over-represented motifs using the MotifSampler implementation of the Gibbs sampler, with higher-order background models
· Detect cis-regulatory modules using the ModuleSearcher web service: the best combination of sites in your set
· Import/export in standard formats (EMBL, fastA, Genbank), and as JPG or PNG images.
· Java 1.4 or later