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External resources - (No support from the ExPASy Team)Showing 4 records out of 4 total
Tagger and fetchGWI are tools which allow searching short sequence tags against entire genomes or mRNA reference sequence databases.
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
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.
TagScan allows searching for exact or near-exact matches between oligonucleotide queries of up to 60 bases and sequence databases comprising entire genomes or mRNA reference sequences. The smallest query allowed is 10 nucleotides long.
keywords: sequence alignment, short sequence alignment