European Bioinformatics Institute

Last updated

European Bioinformatics Institute (EBI)
AbbreviationEMBL-EBI
Formation1992 [1]
Location
Coordinates52.079889, 0.186356
Director
 Ewan Birney
Director
 Rolf Apweiler
Parent organization
 European Molecular Biology Laboratory
Staff
570 [2]
Website www.ebi.ac.uk

The European Bioinformatics Institute (EMBL-EBI) 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. [3] Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics. [4]

Contents

Additionally, the EMBL-EBI hosts training programs that teach scientists the fundamentals of the work with biological data and promote the plethora of bioinformatic tools available for their research, both EMBL-EBI and non-EMBL-EBI-based.

Bioinformatic services

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 is provided, such as Basic Local Alignment Search Tool (BLAST) or Clustal Omega sequence alignment tool, enabling further data analysis.

BLAST

BLAST [5] is an algorithm for the comparison of biomacromolecule primary structure, most often nucleotide sequence of DNA/RNA and amino acid sequence of proteins, stored in the bioinformatic databases, with the query sequence. The algorithm utilizes scoring of the available sequences against 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. [6]

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 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). [7]

Clustal Omega

Clustal Omega [8] 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. [9] Clustal Omega algorithm employs two profile Hidden Markov models (HMMs) to derive 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. [10] The main advantage of Clustal Omega over other MSA tools (Muscle, ProbCons) is its efficiency, while maintaining a significant accuracy of the results.

Ensembl

Based at the EMBL-EBI, the Ensembl [11] 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 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. [12]

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 the sister project Ensembl Genomes. As of 2020, the various Ensembl project databases together house over 50,000 reference genomes. [13]

PDB

PDB [14] 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 NMR spectroscopy, and submitted manually by structural biologists worldwide through PDB member organizations – PDBe, RCSB, PDBj and BMRB. The database can be accessed through the webpages of its members, including PDBe (housed at the EMBL-EBI). As a member of the wwPDB consortium, PDBe aids in the joint mission of archiving and maintenance of macromolecular structure data. [15]

UniProt

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 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. [16]

The protein entries stored in UniProt are cataloged by a unique UniProt identifier. The annotation data collected for 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. [17]

Other bioinformatics organisations

The European Bioinformatics Institute, Hinxton, Cambridge, UK European Bioinformatics Institute, Hinxton 2.jpg
The European Bioinformatics Institute, Hinxton, Cambridge, UK

See also

Related Research Articles

<span class="mw-page-title-main">Sequence alignment</span> Process in bioinformatics that identifies equivalent sites within molecular sequences

In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences such as calculating the distance cost between strings in a natural language, or to display financial data.

<span class="mw-page-title-main">National Center for Biotechnology Information</span> Database branch of the US National Library of Medicine

The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.

In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer. The UniProt database is an example of a protein sequence database. As of 2013 it contained over 40 million sequences and is growing at an exponential rate. Historically, sequences were published in paper form, but as the number of sequences grew, this storage method became unsustainable.

<span class="mw-page-title-main">UniProt</span> Database of protein sequences and functional information

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, United States.

The Protein Information Resource (PIR), located at Georgetown University Medical Center, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies. It contains protein sequences databases

<span class="mw-page-title-main">Ensembl genome database project</span> Scientific project at the European Bioinformatics Institute

Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the retrieval of genomic information.

The Bioinformatic Harvester was a bioinformatic meta search engine created by the European Molecular Biology Laboratory and subsequently hosted and further developed by KIT Karlsruhe Institute of Technology for genes and protein-associated information. Harvester currently works for human, mouse, rat, zebrafish, drosophila and arabidopsis thaliana based information. Harvester cross-links >50 popular bioinformatic resources and allows cross searches. Harvester serves tens of thousands of pages every day to scientists and physicians. Since 2014 the service is down.

InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them.

Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry. The individual resources are hosted in a decentralized way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions.

The Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences and their protein products. RefSeq was introduced in 2000. This database is built by National Center for Biotechnology Information (NCBI), and, unlike GenBank, provides only a single record for each natural biological molecule for major organisms ranging from viruses to bacteria to eukaryotes.

<span class="mw-page-title-main">UGENE</span>

UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.

The UCSC Genome Browser is an online and downloadable genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels. The Genome Browser Database, browsing tools, downloadable data files, and documentation can all be found on the UCSC Genome Bioinformatics website.

<span class="mw-page-title-main">European Nucleotide Archive</span> Online database from the EBI on Nucleotides

The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database. The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the DNA Data Bank of Japan and GenBank.

In bioinformatics, the PANTHER classification system is a large curated biological database of gene/protein families and their functionally related subfamilies that can be used to classify and identify the function of gene products. PANTHER is part of the Gene Ontology Reference Genome Project designed to classify proteins and their genes for high-throughput analysis.

<span class="mw-page-title-main">Zinc finger protein 684</span> Protein found in humans

Zinc finger protein 684 is a protein that in humans is encoded by the ZNF684 gene.

<span class="mw-page-title-main">C17orf50</span> Protein-coding gene in the species Homo sapiens

Uncharacterized protein C17orf50 is a protein which in humans is encoded by the C17orf50 gene.

<span class="mw-page-title-main">C9orf25</span> Protein-coding gene in the species Homo sapiens

Chromosome 9 open reading frame 25 (C9orf25) is a domain that encodes the FAM219A gene. The terms FAM219A and C9orf25 are aliases and can be used interchangeably. The function of this gene is not yet completely understood.

<span class="mw-page-title-main">TMEM169</span> Gene

Transmembrane protein 169 (TMEM169) in humans is encoded by TMEM169 gene. The aliases of TMEM169 include FLJ34263, DKFZp781L2456, and LOC92691. TMEM169 has the highest expression in the brain, particularly the fetal brain. TMEM169 has homologs mammals, reptiles, amphibians, birds, fish, chordates and invertebrates. The most distantly related homolog of TMEM169 is Anopheles albimanus.

<span class="mw-page-title-main">TBC1D30</span> Protein-coding gene in the species Homo sapiens

TBC1D30 is a gene in the human genome that encodes the protein of the same name. This protein has two domains, one of which is involved in the processing of the Rab protein. Much of the function of this gene is not yet known, but it is expressed mostly in the brain and adrenal cortex.

References

  1. ↑ "Background | European Bioinformatics Institute". Ebi.ac.uk. 16 May 2018. Retrieved 29 October 2019.
  2. ↑ "Jobs at EMBL-EBI" . Retrieved 20 June 2016.
  3. ↑ "Scientific report" (PDF). www.embl.de. 2017. Retrieved 29 October 2019.
  4. ↑ BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences. (2018). Annual Report, p. 6. Retrieved 26 March 2020.
  5. ↑ "NCBI BLAST at EMBL-EBI". www.ebi.ac.uk. Retrieved 3 November 2021.
  6. ↑ Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (October 1990). "Basic local alignment search tool". Journal of Molecular Biology. 215 (3): 403–410. doi:10.1016/S0022-2836(05)80360-2. PMID   2231712. S2CID   14441902.
  7. ↑ Wheeler D, Bhagwat M (2007). BLAST QuickStart. Methods in Molecular Biology. Vol. 395. Humana Press. pp. 149–176. PMC   4780883 . PMID   17993672.
  8. ↑ "Clustal Omega at EMBL-EBI". ebi.ac.uk. Retrieved 3 November 2021.
  9. ↑ "Clustal Omega Documentation at EMBL-EBI". ebi.ac.uk. Retrieved 3 November 2021.
  10. ↑ Sievers F, Higgins DG (January 2018). "Clustal Omega for making accurate alignments of many protein sequences". Protein Science. 27 (1): 135–145. doi:10.1002/pro.3290. PMC   5734385 . PMID   28884485.
  11. ↑ "Ensembl homepage". ensembl.org. Retrieved 3 November 2021.
  12. ↑ Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, et al. (January 2021). "Ensembl 2021". Nucleic Acids Research. 49 (D1): D884–D891. doi:10.1093/nar/gkaa942. PMC   7778975 . PMID   33137190.
  13. ↑ "About the Ensembl Project". ensembl.org. Retrieved 3 November 2021.
  14. ↑ Burley, Stephen K.; et al. (January 2019). "Protein Data Bank: the single global archive for 3D macromolecular structure data". Nucleic Acids Research. 47 (D1): D520–D528. doi:10.1093/nar/gky949. PMC   6324056 . PMID   30357364.
  15. ↑ "About PDBe". ebi.ac.uk. Retrieved 3 November 2021.
  16. ↑ "About UniProt". uniprot.org. Retrieved 3 November 2021.
  17. ↑ Bateman, Alex; et al. (January 2021). "UniProt: the universal protein knowledgebase in 2021". Nucleic Acids Research. 49 (D1): D480–D489. doi:10.1093/nar/gkaa1100. PMC   7778908 . PMID   33237286.
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