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Multiple alignment of nucleic acid and protein sequences.
Diagonal plots to graphically compare of biological sequences and identify regions of close similarity
Set of bioinformatics tools, databases and courses
Tagger and fetchGWI are tools which allow searching short sequence tags against entire genomes or mRNA reference sequence databases.
Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models.
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
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.
SIM finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence. Results can be viewed with LALNVIEW, a graphical viewer program for pairwise alignments.
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
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures
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