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Databases

  • neXtProt  •  neXtProt is an innovative knowledge platform dedicated to human proteins. This resource contains a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt is continuously extended so as to provide many more carefully selected data sets and analysis tools. [less]
  • UniProtKB  •  The UniProt Knowledgebase (UniProtKB) 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). [less]
  • UniProtKB/Swiss-Prot  •  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. [less]
  • ViralZone  •  ViralZone is a web resource for all viral genus and families, providing general molecular and epidemiological informations, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. [less]
  • HAMAP  •  HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. HAMAP is applied to bacterial, archaeal and eukaryotic proteins and used to annotate records in UniProtKB via UniProt's automatic annotation pipeline. [less]
  • SwissVar  •  SwissVar is a portal to search variants (polymorphism) in UniProt Knowledgebase (UniProtKB) entries, and gives direct access to manual annotation on the genotype-phenotype relationship of each specific variant based on literature, as well as pre-computed information (such as conservation scores and a list of structural features when available) to help assess the effect of the variant. [less]
  • UniMES (UniProt metagenomic samples)  •  The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data. Currently, unimes.fasta.gz contains only data from the Global Ocean Sampling Expedition (GOS). Clustered sets (unimes_cluster100 and unimes_cluster90) of UniMEs sequences at two resolutions (100% and >90%) are also available. [less]
  • UniRef (UniProt sequence clusters)  •  The UniRef databases provide clustered sets of sequences from UniProt Knowledgebase (including splice variants and isoforms) and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view. [less]

Tools

  • AACompIdent  •  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. [less]
  • Decrease redundancy  •  Redundancy reduction in a set of aligned or unaligned sequences [less]
  • FindPept  •  Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage. [less]
  • GlycoMod  •  Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides. [less]
  • Graphical Codon Usage Analyser  •  Differences in codon usage preference among organisms lead to a variety of problems concerning heterologous gene expression but can be overcome by rational gene design and gene synthesis. The gcua tool displays the codon quality either in codon usage frequency values or relative adaptiveness values [less]
  • HAMAP  •  HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. HAMAP is applied to bacterial, archaeal and eukaryotic proteins and used to annotate records in UniProtKB via UniProt's automatic annotation pipeline. [less]
  • LALIGN  •  LALIGN, from the FASTA package, finds multiple matching subsegments in two sequences, locally or globally. [less]
  • PeptideMass  •  Cleave a protein sequence with a chosen enzyme/protease, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the protein of interest. If desired, PeptideMass can return the mass of peptides known to carry post-translational modifications, and can highlight peptides whose masses may be affected by database conflicts, polymorphisms or splice variants. [less]
  • Reverse Translate  •  Accepts a protein sequence as input and uses a codon usage table to generate a DNA sequence representing the most likely non-degenerate coding sequence. A consensus sequence derived from all the possible codons for each amino acid is also returned.  [less]
  • TagIdent  •  Identify proteins with isoelectric point (pI), molecular weight (Mw) and sequence tag, or generate a list of proteins close to a given pI and Mw. [less]
  • Translate  •  Translation of a nucleotide (DNA/RNA) sequence to a protein sequence. [less]