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Arlequin provides the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples. The graphical interface is designed to allow users to rapidly select the different analyses they want to perform on their data. One can explore the data, and analyze several times the same data set from different perspectives, with different selected options.
BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model.
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.
keywords: Affymetrix chip analysis, animal, arthropod, Bayesian network, ChIP-seq, eukaryotic promoter, expression, expression data, fungi, genetic data analysis, genomics, graphics, HMM, human, insect, in situ hybridization, interaction, maximum likelihood, microarray, network, NGS, regulatory site, sequence analysis, sequencing, transcription factor binding site, transcription module, transcription regulation, transcription start site annotation, transcriptome analysis, vertebrate
miROrtho contains predictions of precursor miRNA genes covering many animal genomes combining evidence from sequence homology and Support Vector Machine classifiers. We provide both consistent extrapolation of already known miRBase families and novel miRNA predictions by our SVM and orthology pipeline.
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