UniProt Sequence Databases

The UniProt KB is an automatically and manually annotated protein database drawn from translation of DDBJ/EMBL-Bank/GenBank coding sequences and directly sequenced proteins. Each sequence receives a imique, stable identifier allowing unambiguous identification of any protein across datasets. The KB also provides cross-references to external data collections such as the underlying DNA sequence entries in the DDBJ/EMBL-Bank/GenBank nucleotide sequence databases, 2D PAGE and 3D protein structure databases, various protein domain... 

Introduction to Molecular Biology Databases. 1994-2004. R. Apweiler, R. Lopez, B. Marx, UniProt, SWISS-PROT, Switzerland. URL http //www.ebi.ac.uk/swissprot/Publications/ mbdl.html. Contents include bibliographic, taxonomy, nucleotide sequence, genetic, and protein sequence databases PIR, SWISS-PROT, and TrEMBL, and specialized protein, protein sequence, secondary protein, and structme databases. 

Field/value-based flat files have been very commonly used in bioinformatics. Examples are the flat file libraries from GenBank, European Molecular Biology Laboratory Nucleotide Sequence Database (EMBL), DNA Data Bank of Japan, or Universal Protein Resource (UniProt). These file types are a very limited solution because they lack referencing, vocabulary control, and constraints. In addition, on the file level, there is no inherent locking mechanism that detects when a file is being used or modified. However, these file types are primarily used for reading purposes. 

In 2002, UniProt consortium (http //www.uniprot.org) was formed by uniting the SWISS-PROT -I- TrEMBL and PIR-PSD activities by maintaining a high-quality database that serves as a stable, comprehensive, fully classified and accurately annotated protein sequence knowledge base (Figure 16.2). The database offers extensive cross-references and querying interfaces fuUy accessible to the scientific community (Bairoch et al., 2005). The UniProt consortium produces three layers of protein sequence databases ... 

The UniProt Reference databases (UniRel) provide nonredundant data collections based on the UniProtKB and UniParc, in order to obtain complete coverage of sequence space at several resolutions. UniRef databases (sequence collections clustered by sequence identity, for performing faster homology searches) are created as representative protein sequence databases witli high information content. 

The Universal Protein Resource (UniProt) provides the scientific community with a centralized, authoritative resource for protein sequences and functional information with three database components. (1) The UniProt Knowledgebase (UniProtKB), produced by a combination of automation and over 25 years of human curation, is the central protein sequence database with accurate, consistent, functional annotation and extensive cross-references. (2) The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from UniProtKB (including splice variants and isoforms) in order to obtain complete coverage of sequence space at several resolutions. The UniRef 100 database is particularly useful for Mass Spec identifications as it exposes known sequence variation and splice-form annotation contained in UniProtKB records. (3) The UniProt Archive (UniParc) provides a stable comprehensive sequence collection by storing the complete body of all publicly available protein sequence data. 

The lower part shows information ofselected protein sequence. The small table shows the results of sequence search against UNIPROT(Swiss-prot/TrEMBL), nr.aa, and UniGene database see Subheading 2, items 2 and 4) using BLAST. 

Other very useful databases (mainly in terms of amino acid sequences in allergens) are the ones which characterize proteins (e.g., The UniProt Knowledgebase— http //expasy.org/sprot/. This database consists of... 

Compare allergenic sequences within the Allergome database and outside in Uniprot... 

BioRDF (Ruttenberg et al. 2007) supports a variety of neurochemical databases, has RDF-ified gene records, databases of receptor-ligand and protein-protein interactions, a directory of commercially available antibodies, Reactome, KEGG, the NCI metathesaurus, and UniProt (which is a collaboration between the SIB in Zurich and the EBI in Hinxton, UK), hence providing a Semantic Web representation of protein sequences. 

The method used by the pathway hole Hlling program PH-Filler (8) is as follows. Given a reaction that is a pathway hole, the program Hrst queries the UniProt database to find all known sequences for enzymes that catalyze that same reaction in other... 

UniProt is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProt is comprised of three components, each optimized for different uses. The UniProt Knowledgebase (UniProt) is the central access point for extensive curated protein information, including function, classification, and cross-reference. The UniProt Non-redundant Reference (UniRef) databases combine closely related sequences into a single record to speed searches. The UniProt Archive (UniParc) is a comprehensive repository, reflecting the history of all protein sequences. 

Search or downlo the UniProt Reference Cluster databases- UniRef coinbines dosely related sequences into a single record tg spaed sequence searches. 

The databases of UniProt are accessible at http //www.uniprot.org/detabase/Databases.shtml which offers searches for UniProtKB, UniRef, UniParc (a comprehensive repository of all sequences) and a download facility. 

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