The European Bioinformatics Institute (EMBL-EBI) is an
intergovernmental organization
Globalization is social change associated with increased connectivity among societies and their elements and the explosive evolution of transportation and telecommunication technologies to facilitate international cultural and economic exchange. ...
(IGO) which, as part of the
European Molecular Biology Laboratory
The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 29 member states, two prospect member states, and one associate member state. EMBL was created in ...
(EMBL) family, focuses on research and services in
bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...
. It is located on the
Wellcome Genome Campus in
Hinxton
Hinxton is a village in South Cambridgeshire, England.
The River Cam runs through the village, as does the Cambridge to Liverpool Street station, Liverpool Street railway, though the village has no station. Hinxton parish's southern boundarie ...
near
Cambridge
Cambridge ( ) is a List of cities in the United Kingdom, city and non-metropolitan district in the county of Cambridgeshire, England. It is the county town of Cambridgeshire and is located on the River Cam, north of London. As of the 2021 Unit ...
, and employs over 600
full-time equivalent
Full-time equivalent (FTE), or whole time equivalent (WTE), is a unit of measurement that indicates the workload of an employed person (or student) in a way that makes workloads or class loads comparable across various contexts. FTE is often use ...
(FTE) staff.
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 is an algorithm for comparing biomacromolecule primary structure, most often nucleotide sequence of
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
/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
In bioinformatics, the BLOSUM (BLOcks SUbstitution Matrix) matrix is a substitution matrix used for sequence alignment of proteins. BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences. They are based o ...
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
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics.
History
The original FASTA program ...
, 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).
Clustal Omega
Clustal
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 . It is available as standalone software, ...
Omega is a
multiple sequence alignment
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis an ...
(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
A hidden Markov model (HMM) is a Markov model in which the observations are dependent on a latent (or ''hidden'') Markov process (referred to as X). An HMM requires that there be an observable process Y whose outcomes depend on the outcomes of X ...
(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. 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 is a database organized around genomic data, maintained by the
Ensembl Project. Tasked with the continuous annotation of the genomes of
model organisms
A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms. Mo ...
, 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.
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
Ensembl Genomes is a scientific project to provide genome-scale data from non-vertebrate species.
The project is run by the European Bioinformatics Institute, and was launched in 2009 using the Ensembl technology. The main objective of the Ense ...
. the various Ensembl project databases together house over 50,000 reference genomes.
PDB
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained a ...
(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
X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract in specific directions. By measuring th ...
or
nuclear magnetic resonance spectroscopy
Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a Spectroscopy, spectroscopic technique based on re-orientation of Atomic nucleus, atomic nuclei with non-zero nuclear sp ...
(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
The Worldwide Protein Data Bank (wwPDB) is an organization that maintains the archive of macromolecular structure. Its mission is to maintain a single Protein Data Bank Archive of macromolecular
A macromolecule is a "molecule of high relat ...
(wwPDB) consortium, PDBe aids in the joint mission of archiving and maintenance of macromolecular structure data.
UniProt
UniProt
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 fro ...
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
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland.
The institute was established on 30 March 1998 and its mission is to provide core bioinform ...
(SIB) (together maintaining Swiss-Prot and TrEMBL) and
Protein Information Resource 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
H ...
(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 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.
AlphaFold DB
The AlphaFold Protein Structure Database (AlphaFold DB) is a collaborative project with
Google DeepMind
DeepMind Technologies Limited, trading as Google DeepMind or simply DeepMind, is a British–American artificial intelligence research laboratory which serves as a subsidiary of Alphabet Inc. Founded in the UK in 2010, it was acquired by Goo ...
to make predicted protein structures from the
AlphaFold
AlphaFold is an artificial intelligence (AI) program developed by DeepMind, a subsidiary of Alphabet, which performs predictions of protein structure. It is designed using deep learning techniques.
AlphaFold 1 (2018) placed first in the overall ...
AI system freely available to the scientific community.
The first release of the database was in 2021; , AlphaFold DB provides access to over 214 million protein structures.
Other bioinformatics organisations
*
National Center for Biotechnology Information
The National Center for Biotechnology Information (NCBI) is part of the 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 lo ...
(NCBI),
United States National Library of Medicine
The United States National Library of Medicine (NLM), operated by the United States federal government, is the world's largest medical library.
Located in Bethesda, Maryland, the NLM is an institute within the National Institutes of Health. I ...
*
National Institute of Genetics (
DNA Data Bank of Japan
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Da ...
)
*
Swiss Institute of Bioinformatics
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland.
The institute was established on 30 March 1998 and its mission is to provide core bioinform ...
(SIB:
Expasy)
*
Australia Bioinformatics Resource
* BIG Data Center (National Genomics Data Center),
Beijing Institute of Genomics Beijing Institute of Genomics (BIG; ) is a genomics research center of Chinese Academy of Sciences (CAS).
History
BIG was officially founded by Yang Huanming, Wang Jian, Yu Jun and others scientists on November 28, 2003, when BGI (formerly the Be ...
,
Chinese Academy of Sciences
The Chinese Academy of Sciences (CAS; ) is the national academy for natural sciences and the highest consultancy for science and technology of the People's Republic of China. It is the world's largest research organization, with 106 research i ...
See also
*
Alternative splicing and transcript diversity database
*
BioJS
BioJS is an open-source project for bioinformatics data on the web. Its goal is to develop an open-source library of JavaScript components to visualise biological data. BioJS develops and maintains small building blocks (components) which can be r ...
- open-source project for
bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...
data on the web
*
BioSamples
*
European Molecular Biology Organization
The European Molecular Biology Organization (EMBO) is a professional, non-profit organization of more than 2,100 life scientists. Its goal is to promote research in life science and enable international exchange between scientists. It co-funds cour ...
*
European Nucleotide Archive
The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated nucleic acid sequence, DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of Genome p ...
References
{{Portal bar, Biology, Europe
Bioinformatics organizations
Biological research institutes in the United Kingdom
Buildings and structures in South Cambridgeshire District
Hinxton
Information technology organizations based in Europe
International research institutes
Molecular biology institutes
Partner institutions of the University of Cambridge
Research institutes established in 1992
Research institutes in Cambridgeshire
Science and technology in Europe
Systems science institutes
1992 establishments in England