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Showing 11 records out of 11 total
BLAST sequence similarity search (blastp or tblastn) against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB, EMBL, ESTs
keywords: similarity search
Set of bioinformatics tools, databases and courses
HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.
Scan several sequences or a whole genome (all ORFs) against the HAMAP families, with partial or complete annotation in UniProtKB/Swiss-Prot format.
LALIGN, from the FASTA package, finds multiple matching subsegments in two sequences, locally or globally.
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.
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
A data mining solution to map thousands of viral isolates
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