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Protein identification by amino acid composition, and optionally pI, Mw, species, UniProtKB keyword and calibration protein. Several constellations are available, corresponding to various amino acid analysis techniques.
Compare amino acid composition of a UniProtKB entry with some or all other UniProtKB entries. Several constellations are available, corresponding to various amino acid analysis techniques.
The AllAll server takes as input a set of protein sequences and returns various comparisons and visualizations- a distance-based phylogenetic tree, a split tree, some variation indices, some visualizations, the pairwise sequence distances and the most probable ancestral sequence.
Redundancy reduction in a set of aligned or unaligned sequences
Diagonal plots to graphically compare of biological sequences and identify regions of close similarity
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
A data mining solution to map thousands of viral isolates
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
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