Search for Resources Advanced Search
SIB resources
External resources - (No support from the ExPASy Team)Showing 5 records out of 5 total
The ChIP-Seq tools are used to analyze ChIP-seq data and other types of mass genome annotation data (MGA).The programs are: a feature correlation tool (ChIP-cor); a tag centering tool (ChIP-center); a signal peak detection tool (ChIP-peak and a partitioning tool (ChIP-part)
MARA models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets.
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.
keywords: alignment analysis, Bayesian network, ChIP-seq, hidden markov model (HMM), maximum likelihood, model of evolution, network, next generation sequencing (NGS), sequence alignment, sequence analysis, short sequence alignment, transcription factor binding site, transcription module, transcription regulation
Software to analyse deep-sequencing (NGS) data and reconstruct haplotypes in a genetically heterogeneous sample
SwissRegulon is a database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a clear and comprehensible graphical form.