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26-520: 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. Similar databases and browsers are found at NCBI and

52-523: A compact and index-able representation of nucleotide sequence alignments. The goal of indexing is to retrieve alignments that overlap a specific location quickly without having to go through all of them. Before indexing, BAM must be sorted by reference ID and then leftmost coordinate. BAM is in compressed BGZF format. The structure of BAM files include a header section and an alignment section: Bam format uses 0-based coordinate system , where as SAM uses 1-based coordinate system. BAM can represent values in

78-586: 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

104-456: 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). Clustal Omega

130-468: A new website designed to make genome annotation data available more quickly to users, and COVID-19 , a new website to access to SARS-CoV-2 reference genome. Central to the Ensembl concept is the ability to automatically generate graphical views of the alignment of genes and other genomic data against a reference genome . These are shown as data tracks, and individual tracks can be turned on and off, allowing

156-418: A range of species. The graphics are complemented by tabular displays, and in many cases data can be exported directly from the page in a variety of standard file formats such as FASTA . Externally produced data can also be added to the display by uploading a suitable file in one of the supported formats, such as BAM , BED , or PSL . Graphics are generated using a suite of custom Perl modules based on GD ,

182-440: A sister project, Ensembl Genomes , has extended the scope of Ensembl into invertebrate metazoa , plants , fungi , bacteria , and protists , focusing on providing taxonomic and evolutionary context to genes, whilst the original project continues to focus on vertebrates. As of 2020, Ensembl supported over 50 000 genomes across both Ensembl and Ensembl Genomes databases, adding some new innovative features such as Rapid Release ,

208-479: 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 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

234-454: 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. BAM (file format) BAM is the compressed binary representation of SAM (Sequence Alignment Map),

260-519: Is a slow, painstaking task. The alternative, known as automated annotation, is to use the power of computers to do the complex pattern-matching of protein to DNA . The Ensembl project was launched in 1999 in response to the imminent completion of the Human Genome Project , with the initial goals of automatically annotate the human genome, integrate this annotation with available biological data and make all this knowledge publicly available. In

286-428: Is also a publicly accessible database server allowing remote access. In addition, the Ensembl website provides computer-generated visual displays of much of the data. Over time the project has expanded to include additional species (including key model organisms such as mouse , fruitfly and zebrafish ) as well as a wider range of genomic data, including genetic variations and regulatory features. Since April 2009,

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312-514: 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. The database search by BLAST requires input data to be in

338-729: 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 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

364-420: The Ensembl project is open access and all software is open source, being freely available to the scientific community, under a CC BY 4.0 license. Currently, Ensembl database website is mirrored at four different locations worldwide to improve the service. European Bioinformatics Institute The European Bioinformatics Institute ( EMBL-EBI ) is an intergovernmental organization (IGO) which, as part of

390-465: The Ensembl project, sequence data are fed into the gene annotation system (a collection of software "pipelines" written in Perl ) which creates a set of predicted gene locations and saves them in a MySQL database for subsequent analysis and display. Ensembl makes these data freely accessible to the world research community. All the data and code produced by the Ensembl project is available to download, and there

416-717: The MySQL with direct SQL queries, but this requires an extensive knowledge of the current database schema. Large datasets can be retrieved using the BioMart data-mining tool. It provides a web interface for downloading datasets using complex queries. Last, there is an FTP server which can be used to download entire MySQL databases as well some selected data sets in other formats. The annotated genomes include most fully sequenced vertebrates and selected model organisms. All of them are eukaryotes, there are no prokaryotes. As of 2022, there are 271 species registered, this includes: All data part of

442-504: The University of California, Santa Cruz (UCSC) . The human genome consists of three billion base pairs , which code for approximately 20,000–25,000 genes . However the genome alone is of little use, unless the locations and relationships of individual genes can be identified. One option is manual annotation , whereby a team of scientists tries to locate genes using experimental data from scientific journals and public databases. However this

468-466: The compara API (for comparative genomics data), the variation API (for accessing SNPs, SNVs, CNVs..), and the functional genomics API (to access regulatory data). The Ensembl website provides extensive information on how to install and use the API . This software can be used to access the public MySQL database, avoiding the need to download enormous datasets. The users could even choose to retrieve data from

494-578: 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)

520-687: 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. 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

546-609: 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

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572-487: 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, 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

598-459: 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

624-404: The standard Perl graphics display library. In addition to its website, Ensembl provides a REST API and a Perl API (Application Programming Interface) that models biological objects such as genes and proteins, allowing simple scripts to be written to retrieve data of interest. The same API is used internally by the web interface to display the data. It is divided in sections like the core API,

650-415: The user to customise the display to suit their research interests. The interface also enables the user to zoom in to a region or move along the genome in either direction. Other displays show data at varying levels of resolution, from whole karyotypes down to text-based representations of DNA and amino acid sequences, or present other types of display such as trees of similar genes ( homologues ) across

676-646: 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

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