European Bioinformatics Institute

Last updated

European Bioinformatics Institute (EBI)
AbbreviationEMBL-EBI
Formation1992 [1]
Location
Coordinates52.079889, 0.186356
Director
 Ewan Birney [2]
Associate Director
 Rolf Apweiler [2]
Parent organization
 European Molecular Biology Laboratory
Staff
685 [3]
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. [4]

Contents

Further, 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-based and not so.

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 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 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

Protein Data Bank (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 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 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. [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]

AlphaFold DB

The AlphaFold Protein Structure Database (AlphaFold DB) is a collaborative project with Google DeepMind to make predicted protein structures from the AlphaFold AI system freely available to the scientific community. [18] The first release of the database was in 2021; as of 2024, AlphaFold DB provides access to over 214 million protein structures. [19]

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">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, USA.

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">Clustal</span> Bioinformatics computer program

Clustal is a computer program used for multiple sequence alignment in bioinformatics. The software and its algorithms have gone through several iterations, with ClustalΩ (Omega) being the latest version as of 2011. It is available as standalone software, via a web interface, and through a server hosted by the European Bioinformatics Institute.

<span class="mw-page-title-main">Amos Bairoch</span> Swiss bioinformatician

Amos Bairoch is a Swiss bioinformatician and Professor of Bioinformatics at the Department of Human Protein Sciences of the University of Geneva where he leads the CALIPHO group at the Swiss Institute of Bioinformatics (SIB) combining bioinformatics, curation, and experimental efforts to functionally characterize human proteins.

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.

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> Computer software for bioinformatics

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.

<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">C16orf46</span> Human gene

Chromosome 16 open reading frame 46 is a protein of yet to be determined function in Homo sapiens. It is encoded by the C16orf46 gene with NCBI accession number of NM_001100873. It is a protein-coding gene with an overlapping locus.

<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">C16orf86</span> Protein-coding gene in the species Homo sapiens

Uncharacterized protein C16orf86 is a protein in humans that is encoded by the C16orf86 gene. It is mostly made of alpha helices and it is expressed in the testes, but also in other tissues such as the kidney, colon, brain, fat, spleen, and liver. For the function of C16orf86, it is not well understood, however it could be a transcription factor in the nucleus that regulates G0/G1 in the cell cycle for tissues such as the kidney, brain, and skeletal muscles as mentioned in the DNA microarray data below in the gene level regulation section.

Chromosome 1 open reading frame (C1orf167) is a protein which in humans is encoded by the C1orf167 gene. The NCBI accession number is NP_001010881. The protein is 1468 amino acids in length with a molecular weight of 162.42 kDa. The mRNA sequence was found to be 4689 base pairs in length.

Protein Data Bank in Europe – Knowledge Base (PDBe-KB) is a community-driven, open-access, integrated resource whose mission is to place macromolecular structure data in their biological context and to make them accessible to the scientific community in order to support fundamental and translational research and education. It is part of the European Bioinformatics Institute (EMBL-EBI), based at the Wellcome Genome Campus, Hinxton, Cambridgeshire, England.

<span class="mw-page-title-main">SAAL1</span> Protein-coding gene in the species Homo sapiens

Serum amyloid A-like 1 is a protein in humans encoded by the SAAL1 gene.

<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">FAM214B</span> Protein-coding gene in the species Homo sapiens

The FAM214B, also known as protein family with sequence similarity 214, B (FAM214B) is a protein that, in humans, is encoded by the FAM214B gene located on the human chromosome 9. The protein has 538 amino acids. The gene contain 9 exon. There has been studies that there are low expression of this gene in patients with major depression disorder. In most organisms such as mammals, amphibians, reptiles, and birds, there are high levels of gene expression in the bone marrow and blood. For humans in fetal development, FAM214B is mostly expressed in the brains and bone marrow.

<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.

<span class="mw-page-title-main">ZFP62</span> Gene in Humans

Zinc Finger Protein 62, also known as "ZNF62," "ZNF755," or "ZET," is a protein that in humans is encoded by the ZFP62 gene. ZFP62 is part of the C2H2 Zinc Finger family of genes.

References

  1. ↑ "Background | European Bioinformatics Institute". Ebi.ac.uk. 16 May 2018. Retrieved 29 October 2019.
  2. 1 2 "Leadership". www.ebi.ac.uk. Retrieved 21 August 2024.
  3. ↑ "EMBL-EBI Highlights 2023" (PDF) (Press release). EMBL-EBI. 8 April 2024. p. 4.
  4. ↑ "Scientific report" (PDF). www.embl.de. 2017. Retrieved 29 October 2019.
  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.
  18. ↑ "AlphaFold Protein Structure Database". alphafold.ebi.ac.uk. Retrieved 22 August 2024.
  19. ↑ Varadi, Mihaly; Bertoni, Damian; Magana, Paulyna; Paramval, Urmila; Pidruchna, Ivanna; Radhakrishnan, Malarvizhi; Tsenkov, Maxim; Nair, Sreenath; Mirdita, Milot; Yeo, Jingi; Kovalevskiy, Oleg; Tunyasuvunakool, Kathryn; Laydon, Agata; Žídek, Augustin; Tomlinson, Hamish; Hariharan, Dhavanthi; Abrahamson, Josh; Green, Tim; Jumper, John; Birney, Ewan; Steinegger, Martin; Hassabis, Demis; Velankar, Sameer (5 January 2024). "AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences". Nucleic Acids Research. 52 (D1): D368–D375. doi:10.1093/nar/gkad1011. PMC   10767828 .
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