Search for SIB Resources Advanced Search
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, alignment analysis, animal, arthropod, Bayesian network, binding sites prediction, C, ChIP-seq, evolution, fungi, genetic data analysis, genomics, Gibbs sampler, HMM, human, insect, interaction, maximum likelihood, model of evolution, multiple sequence alignment (MSA), network, NGS, phylogibbs, population genetics, regulatory site, selection, sequence analysis, sequence comparison, short sequence alignment, similarity search, transcription factor binding site, transcription module, transcription regulation, transcriptome analysis, vertebrate
Swissregulon is a database of genome-wide annotations of regulatory sites. Swissregulon contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offer easy and intuitive interface showing genomic information in clear and comprehensible graphical form.
keywords: alignment, animal, arthropod, bacteria, binding sites prediction, ChIP-seq, database searching, eukaryotic promoter, fungi, genetic data analysis, genomics, graphics, human, insect, in situ hybridization, interaction, kinase regulator interaction, multiple sequence alignment (MSA), network, NGS, population genetics, protein interaction, regulatory site, selection, sequence analysis, sequence comparison, sequence retrieval, short sequence alignment, transcription factor binding site, transcription module, transcription regulation, transcription start site annotation, transcriptome analysis, two component system, vertebrate
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: alignment, animal, arthropod, fast sequence matching, genomics, human, insect, short sequence alignment, vertebrate