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34-955: The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy (Expert Protein Analysis System) servers that are

68-776: A central resource for proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation (NBRF) at the Georgetown University Medical Center in Washington, DC, US, is heir to the oldest protein sequence database, Margaret Dayhoff 's Atlas of Protein Sequence and Structure, first published in 1965. In 2002, EBI, SIB, and PIR joined forces as the UniProt consortium. Each consortium member

102-769: A pace exceeding Swiss-Prot's ability to keep up, TrEMBL (Translated EMBL Nucleotide Sequence Data Library) was created to provide automated annotations for those proteins not in Swiss-Prot. Meanwhile, PIR maintained the PIR-PSD and related databases, including iProClass , a database of protein sequences and curated families. The consortium members pooled their overlapping resources and expertise, and launched UniProt in December 2003. UniProt provides four core databases: UniProtKB (with sub-parts Swiss-Prot and TrEMBL), UniParc, UniRef and Proteome. UniProt Knowledgebase (UniProtKB)

136-527: A representative protein, the accession numbers of all the merged entries and links to the corresponding UniProtKB and UniParc records are displayed. UniRef100 sequences are clustered using the CD-HIT algorithm to build UniRef90 and UniRef50. Each cluster is composed of sequences that have at least 90% or 50% sequence identity, respectively, to the longest sequence. Clustering sequences significantly reduces database size, enabling faster sequence searches. UniRef

170-411: A web browser. The stored data can be interacted with using a graphical UI, which supports the display of data in multiple resolution levels from karyotype, through individual genes, to nucleotide sequence. Originally centered on vertebrate animals as its main field of interest, since 2009 Ensembl provides annotated data regarding the genomes of plants, fungi, invertebrates, bacteria and other species, in

204-516: Is a collaborative project with Google DeepMind to make predicted protein structures from the AlphaFold AI system freely available to the scientific community. The first release of the database was in 2021; as of 2024 , AlphaFold DB provides access to over 214 million protein structures. Membrane topology Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect to

238-442: Is a comprehensive and non-redundant database, which contains all the protein sequences from the main, publicly available protein sequence databases. Proteins may exist in several different source databases, and in multiple copies in the same database. In order to avoid redundancy, UniParc stores each unique sequence only once. Identical sequences are merged, regardless of whether they are from the same or different species. Each sequence

272-424: Is a manually annotated, non-redundant protein sequence database. It combines information extracted from scientific literature and biocurator -evaluated computational analysis. The aim of UniProtKB/Swiss-Prot is to provide all known relevant information about a particular protein. Annotation is regularly reviewed to keep up with current scientific findings. The manual annotation of an entry involves detailed analysis of

306-555: Is a protein database partially curated by experts, consisting of two sections: UniProtKB/Swiss-Prot (containing reviewed, manually annotated entries) and UniProtKB/TrEMBL (containing unreviewed, automatically annotated entries). As of 22 February 2023, release "2023_01" of UniProtKB/Swiss-Prot contains 569,213 sequence entries (comprising 205,728,242 amino acids abstracted from 291,046 references) and release "2023_01" of UniProtKB/TrEMBL contains 245,871,724 sequence entries (comprising 85,739,380,194 amino acids). UniProtKB/Swiss-Prot

340-678: Is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics . It is located on the Wellcome Genome Campus in Hinxton near Cambridge , and employs over 600 full-time equivalent (FTE) staff. Further, the EMBL-EBI hosts training programs that teach scientists the fundamentals of

374-402: Is archived. Currently UniParc contains protein sequences from the following publicly available databases: The UniProt Reference Clusters (UniRef) consist of three databases of clustered sets of protein sequences from UniProtKB and selected UniParc records. The UniRef100 database combines identical sequences and sequence fragments (from any organism ) into a single UniRef entry. The sequence of

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408-926: Is available from the UniProt FTP site . UniProt is funded by grants from the National Human Genome Research Institute , the National Institutes of Health (NIH), the European Commission , the Swiss Federal Government through the Federal Office of Education and Science, NCI-caBIG , and the US Department of Defense. European Bioinformatics Institute The European Bioinformatics Institute ( EMBL-EBI )

442-486: Is given a stable and unique identifier (UPI), making it possible to identify the same protein from different source databases. UniParc contains only protein sequences, with no annotation. Database cross-references in UniParc entries allow further information about the protein to be retrieved from the source databases. When sequences in the source databases change, these changes are tracked by UniParc and history of all changes

476-557: Is heavily involved in protein database maintenance and annotation. Until recently, EBI and SIB together produced the Swiss-Prot and TrEMBL databases, while PIR produced the Protein Sequence Database (PIR-PSD). These databases coexisted with differing protein sequence coverage and annotation priorities. Swiss-Prot was created in 1986 by Amos Bairoch during his PhD and developed by the Swiss Institute of Bioinformatics and subsequently developed by Rolf Apweiler at

510-420: Is provided, such as Basic Local Alignment Search Tool (BLAST) or Clustal Omega sequence alignment tool, enabling further data analysis. BLAST is an algorithm for comparing biomacromolecule primary structure, most often nucleotide sequence of DNA /RN, and amino acid sequence of proteins, stored in the bioinformatic databases, with the query sequence. The algorithm uses scoring of the available sequences against

544-412: Is read, and information is extracted and added to the entry. Annotation arising from the scientific literature includes, but is not limited to: Annotated entries undergo quality assurance before inclusion into UniProtKB/Swiss-Prot. When new data becomes available, entries are updated. UniProtKB/TrEMBL contains high-quality computationally analyzed records, which are enriched with automatic annotation. It

578-448: Is used in the annotation of UniProtKB/Swiss-Prot entries. Computer-predictions are manually evaluated, and relevant results selected for inclusion in the entry. These predictions include post-translational modifications, transmembrane domains and topology , signal peptides , domain identification, and protein family classification. Relevant publications are identified by searching databases such as PubMed . The full text of each paper

612-409: The European Bioinformatics Institute . Swiss-Prot aimed to provide reliable protein sequences associated with a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications , variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recognizing that sequence data were being generated at

646-568: The Ensembl is a database organized around genomic data, maintained by the Ensembl Project . Tasked with the continuous annotation of the genomes of model organisms , Ensembl provides researchers a comprehensive resource of relevant biological information about each specific genome. The annotation of the stored reference genomes is automatic and sequence-based. Ensembl encompasses a publicly available genome database which can be accessed via

680-586: The each entry are organized in logical sections (e.g. protein function, structure, expression, sequence or relevant publications), allowing a coordinated overview about the protein of interest. Links to external databases and original sources of data are also provided. In addition to standard search by the protein name/identifier, UniProt webpage houses tools for BLAST searching, sequence alignment or searching for proteins containing specific peptides. The AlphaFold Protein Structure Database (AlphaFold DB)

714-474: The fact that membrane-spanning regions contain more hydrophobic residues than other parts of the protein, however applying different hydrophobic scales altered the prediction results. Later, several statistical methods were developed to improve the topography prediction and a special alignment method was introduced. According to the positive-inside rule, cytosolic loops near the lipid bilayer contain more positively-charged amino acids. Applying this rule resulted in

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748-474: The final alignment of the sequences. The output of the Clustal Omega may be visualized in a guide tree (the phylogenetic relationship of the best-pairing sequences) or ordered by the mutual sequence similarity between the queries. The main advantage of Clustal Omega over other MSA tools (Muscle, ProbCons ) is its efficiency, while maintaining a significant accuracy of the results. Based at the EMBL-EBI,

782-499: The final topology) and automatically incorporate previously determined experimental informations. HTP database provides a collection of topologies that are computationally predicted for human transmembrane proteins. Discrimination of signal peptides and transmembrane segments is an additional problem in topology prediction treated with a limited success by different methods. Both signal peptides and transmembrane segments contain hydrophobic regions which form α-helices. This causes

816-460: The first topology prediction methods. There is also a negative-outside rule in transmembrane alpha-helices from single-pass proteins, although negatively charged residues are rarer than positively charged residues in transmembrane segments of proteins. As more structures were determined, machine learning algorithms appeared. Supervised learning methods are trained on a set of experimentally determined structures, however, these methods highly depend on

850-576: The individual ventures of EMBL-EBI, Swiss Institute of Bioinformatics (SIB) (together maintaining Swiss-Prot and TrEMBL) and Protein Information Resource (PIR) (housing Protein Sequence Database), the increase in the global protein data generation led to their collaboration in the creation of UniProt in 2002. The protein entries stored in UniProt are cataloged by a unique UniProt identifier. The annotation data collected for

884-483: The inner or outer sides of the biological membrane occupied by the protein. Several databases provide experimentally determined topologies of membrane proteins. They include Uniprot , TOPDB, OPM , and ExTopoDB. There is also a database of domains located conservatively on a certain side of membranes, TOPDOM. Several computational methods were developed, with a limited success, for predicting transmembrane alpha-helices and their topology. Pioneer methods utilized

918-416: The protein sequence and of the scientific literature. Sequences from the same gene and the same species are merged into the same database entry. Differences between sequences are identified, and their cause documented (for example alternative splicing , natural variation , incorrect initiation sites, incorrect exon boundaries, frameshifts , unidentified conflicts). A range of sequence analysis tools

952-432: The query by a scoring matrix such as BLOSUM 62. The highest scoring sequences represent the closest relatives of the query, in terms of functional and evolutionary similarity. The database search by BLAST requires input data to be in a correct format (e.g. FASTA , GenBank, PIR or EMBL format). Users may also designate the specific databases to be searched, select scoring matrices to be used and other parameters prior to

986-616: The sister project Ensembl Genomes . As of 2020, the various Ensembl project databases together house over 50,000 reference genomes. Protein Data Bank (PDB) is a database of three dimensional structures of biological macromolecules, such as proteins and nucleic acids. The data are typically obtained by X-ray crystallography or nuclear magnetic resonance spectroscopy (NMR spectroscopy), and submitted manually by structural biologists worldwide through PDB member organizations – PDBe , RCSB, PDBj and BMRB. The database can be accessed through

1020-514: The tool run. The best hits in the BLAST results are ordered according to their calculated E-value (the probability of the presence of a similarly or higher-scoring hit in the database by chance). Clustal Omega is a multiple sequence alignment (MSA) tool that enables to find an optimal alignment of at least three and maximum of 4000 input DNA and protein sequences. Clustal Omega algorithm employs two profile Hidden Markov models (HMMs) to derive

1054-493: The training set. Unsupervised learning methods are based on the principle that topology depends on the maximum divergence of the amino acid distributions in different structural parts. It was also shown that locking a segment location based on prior knowledge about the structure improves the prediction accuracy. This feature has been added to some of the existing prediction methods. The most recent methods use consensus prediction (i.e. they use several algorithms to determine

UniProt - Misplaced Pages Continue

1088-671: The webpages of its members, including PDBe (housed at the EMBL-EBI). As a member of the Worldwide Protein Data Bank (wwPDB) consortium, PDBe aids in the joint mission of archiving and maintenance of macromolecular structure data. UniProt is an online repository of protein sequence and annotation data, distributed in UniProt Knowledgebase (UniProt KB), UniProt Reference Clusters (UniRef) and UniProt Archive (UniParc) databases. Originally conceived as

1122-462: The work with biological data and promote the plethora of bioinformatic tools available for their research, both EMBL-EBI-based and not so. One of the roles of the EMBL-EBI is to index and maintain biological data in a set of databases, including Ensembl (housing whole genome sequence data), UniProt (protein sequence and annotation database) and Protein Data Bank (protein and nucleic acid tertiary structure database). A variety of online services and tools

1156-766: Was introduced in response to increased dataflow resulting from genome projects, as the time- and labour-consuming manual annotation process of UniProtKB/Swiss-Prot could not be broadened to include all available protein sequences. The translations of annotated coding sequences in the EMBL-Bank/GenBank/DDBJ nucleotide sequence database are automatically processed and entered in UniProtKB/TrEMBL. UniProtKB/TrEMBL also contains sequences from PDB , and from gene prediction, including Ensembl , RefSeq and CCDS . Since 22 July 2021 it also includes structures predicted with AlphaFold2 . UniProt Archive (UniParc)

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