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Showing 15 records out of 15 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)
The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references.
Tagger and fetchGWI are tools which allow searching short sequence tags against entire genomes or mRNA reference sequence databases.
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.
OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. Available protein descriptors, together with Gene Ontology and InterPro attributes, serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive database querying.
keywords: animal, arthropod, evolution, evolutionary relation, family database, functional annotation, fungi, genomics, homology, human, insect, orthology, paralogy, protein characterization, protein database, protein family, protein function, proteome database, sequence characterisation, sequence retrieval, vertebrate
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
Publication électronique (en français) de vulgarisation scientifique du groupe Swiss-Prot de l'Institut Suisse de Bioinformatique dédiée aux protéines qui font parler d'elles dans l'actualité.
Protein Spotlight is a monthly review written by the Swiss-Prot team of the Swiss Institute of Bioinformatics. Spotlight articles describe a specific protein or family of proteins on an informal tone.
Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment.
The SWISS-2DPAGE database assembles data on proteins identified on various 2-D PAGE and SDS-PAGE maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data and bibliographical references. In addition several 2-D PAGE and SDS-PAGE images are provided, showing the experimentally determined location of the protein, as well as a theoretical region where the protein might be found in the gel.
keywords: 2-D PAGE, animal, bacteria, database searching, disease, experimentally verified, fungi, gel electrophoresis, human, identification, knowledge resource, Make2ddb, mass spectrometry, MW, peptide mass fingerprinting, pI, post-translational modification, protein database, protein identification, proteome database, Swiss-Prot, vertebrate, visualization
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
The UniProt Knowledgebase (UniProtKB) is produced by the UniProt consortium composed of EBI (Rolf Apweiler), PIR (Cathy Wu) and SIB (Swiss-Prot group, Ioannis Xenarios). It is the central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. It consists of: UniProtKB/Swiss-Prot (manually-annotated records and curator-evaluated computational analysis) and UniProtKB/TrEMBL (computationally analyzed records awaiting manual annotation).
keywords: alignment, animal, arthropod, bacteria, cofactor, coiled-coils, database searching, disease, disease mutation, enzyme, experimentally verified, functional annotation, fungi, gene name, glycosylation, homology, human, influenza, insect, interaction, knowledge resource, oligosaccharide, pathogen, pathway, PDB, peptide, physico-chemical property, post-translational modification, primary structure, protein, protein characterization, protein database, protein domain, protein family, protein function, protein interaction, protein name, protein structure, protein variation, proteome database, quaternary structure, reaction, secondary structure, sequence analysis, sequence characterisation, sequence comparison, sequence retrieval, similarity search, Swiss-Prot, taxonomy, tertiary structure, trans-membrane, translation, TrEMBL, vertebrate, virus
UniProtKB/Swiss-Prot is the manually annotated component of UniProtKB. It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis.
keywords: alignment, animal, arthropod, bacteria, biochemical characterization, catalytic activity, classification, cofactor, coiled-coils, database searching, disease, disease mutation, enzyme, experimentally verified, expression data, family database, functional annotation, fungi, gene name, glycosylation, homology, human, influenza, insect, interaction, knowledge resource, pathway, PDB, peptide, physico-chemical property, post-translational modification, primary structure, protein, protein characterization, protein database, protein domain, protein family, protein function, protein interaction, protein name, protein structure, protein variation, quaternary structure, reaction, secondary structure, sequence analysis, sequence characterisation, sequence comparison, sequence retrieval, similarity search, Swiss-Prot, synonym, taxonomy, tertiary structure, topology prediction, trans-membrane, vertebrate, virus