Pham yang embl-ebi
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EMBL-EBI is a free molecular database that provides comprehensive information across various life science domains. It draws data from multiple external sources and databases to offer detailed information on topics like nucleotide sequences, protein structures, genomes, and related literature. Users can access this data online through the EMBL-EBI website and search tools or download selected data and software for offline use.
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Pham yang embl-ebi
- 2. EMBL-EBI Home Page ● EMBL-EBI is a free to use molecular database. It draws from a variety of different databases to provide detailed information about molecular biology. ● The data provided ranges from nucleotide sequences to full systems. ● EMBL-EBI provides links to external websites and databases where more information and files can be found. ● Users can work offline by downloading EBI’s data and software or work online by using their web services. ● Principles ○ Open, Compatible, Comprehensive, Portable, and High Quality http://www.ebi.ac.uk/
- 3. Services ● Various data resources and analysis tools that cover all life science information ● Within each domain service, there are more services and tools that fall under that category ● Free to the public worldwide “Bioinformatics Challenges for the Life Sciecnces”<https://rd-alliance.org/>
- 4. Services “Bioinformatics Challenges for the Life Sciecnces”<https://rd-alliance.org/>
- 5. Search Bar • Using the search bar, type in the desired gene or protein. • This will search through a variety of databases and provide the most relevant information. • Databases include Ensembl, PDBe, Europe PubMed, and many more.
- 6. Search Results For HBA1 Outline • Gene & Protein Summary • Molecular Structures • Genomes • Nucleotide Sequences • Protein Sequences • Literature • Reactions Pathways & Diseases • Small Molecules • Gene Expression • Molecular Interactions • Protein Families • Samples http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&t=HBA1
- 7. Gene & Protein Summary Back to Search Results • The Gene & Protein Summary provides information of the: • Gene • Expression • Protein • Protein Structure • Literature • Here, it can direct us to the gene sequence in Ensembl, the molecular structure in PDBe, and related literature. • http://www.ebi.ac.uk/s4/summary/molecular/gene?term=HB A1&classification=9606&tid=nameOrgENSG00000206172
- 8. Macromolecular Structure Back to Search Results ● The protein structure tab provides an overview and resources for the protein’s structure. ● It includes all related structures to the gene and provides external links to PDBe. http://www.ebi.ac.uk/s4/summary/molecular/structure?term=H BA1&classification=9606&tid=nameOrgENSG00000206172
- 9. Macromolecular Structure Back to Search Results ● Redirected to Protein Data Bank in Europe (PDBe) ● Provides an archive of experimentally determined 3D structures for biological macromolecules http://www.ebi.ac.uk/s4/jump?from=aHR0cDovL3d3dy5lYmkuYWMudWsvczQvc3VtbWFyeS9t b2xlY3VsYXIvc3RydWN0dXJlP3JlZj0xYnowJnRlcm09SEJBMSZjbGFzc2lmaWNhdGlvbj05NjA 2JnRpZD1uYW1lT3JnRU5TRzAwMDAwMjA2MTcy&hash=hash&url=http://www.ebi.ac.uk/pdb e/entry/search/index?pubmed_id:8448109
- 10. Genome Back to Search Results ● The genome section will redirect to Ensembl, where information about the gene can be found. ● Here you can find the proteins corresponding to the HBA1 gene and the gene location. http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=c ore;g=ENSG00000206172;r=16:176680-177522
- 11. Nucleotide Sequence Back to Search Results ● The Nucleotide Sequence provides an overview of the sequence and links to other services. ● This page includes links to HGNC, InterPro, PDBe, UniProtKB/Swiss-Pro, and GOA. ● The FASTA file is also available for download here to use with other programs such as Chimera. http://www.ebi.ac.uk/ena/data/view/AAK6 1216
- 12. Protein Sequence Back to Search Results ● Redirected to Universal Protein Resource (UniProt) ● Comprehensive catalog of information on proteins including: ○ Function ○ Subcellular location ○ Pathology ○ Processing (Molecular processing) (Amino acid modifications) ○ Interactions ○ Structure ○ Sequence ○ Etc http://www.uniprot.org/uniprot/P699 05
- 13. Literature Back to Search Results • The Literature tab provides all related articles and patents to the search term. • These can be filtered by the publication date. • Literature can also be found in the Gene & Protein summary. • EMBL-EBI draws literature from the Europe PMC database. http://www.ebi.ac.uk/s4/summary/molecular/literature?term=H BA1&classification=9606&tid=nameOrgENSG00000206172
- 14. Training Back to Search Results • If you are having trouble using the website, they also provide a free training course on how to navigate their database. http://www.ebi.ac.uk/training/online/
Hinweis der Redaktion
- Through many collaborations, EMBL-EBI has provided various data resources and analysis tools that cover all life science information. First, in order to get the information, labs around the world send over their data. From there, the data is archived, classified, and shared with other data providers to be shown to the general public. In some cases, some data are further analyzed with values added and integrated into the system. To help researchers further analyze the data, tools/programs are then provided to help researchers worldwide analyze the data needed to contribute to their research. Ultimately from there, the cycle all over again. As shown on the slide. EMBL-EBI provides a wide array of services that are categorized into nine domains. These main nine domains are: DNA&RNA, gene expression , proteins, structures, systems, chemical biology, ontologies, literature search, and cross domain. From there, they can be further broken down into other websites and tools that fall under that category.
- As stated in the previous slide, within each of the nine domains are various other websites and analysis tools used to help the user find the desired information. For example, if you wanted to look into a nucleotide sequence, examples of websites provided are the european nucleotide archive, ensembl, etc. If you wanted to look into the molecular structure, there’s the protein data bank or the electron microscopy data bank. What’s shown here is only a sample of what services are provided. The list goes on. Essentially, EMBL-EBI is the central hub for all of these resources to be accessed under one website for researchers worldwide.
- From the search page, clicking the gene and protein summary provides an overall summary or preview of the gene, expression, protein, protein structure, and related literature all in one comprehensive area. If more information is needed, links of the desired information are provided and will redirect you to the website the information came from. In this powerpoint, we decided to limit our search to humans, but you could limit your search to other organisms, like mice. Through this, you can determine the gene sequence (provided by Ensembl), the molecular structure (provided by PDBe), and other related literature.
- http://www.ebi.ac.uk/pdbe/entry/pdb/1bz0 Now, let’s say you wanted to look further into the molecular structure of HBA1. By clicking the protein structure tab on the Gene & protein summary page, an overview of the resources for that protein’s structure is shown. It includes all related structures to that search term and provides external links to the website PDBe. In this case, we decided to look into hemoglobin A (Human, deoxy, high salt)
- http://www.ebi.ac.uk/pdbe/entry/pdb/1bz0 By selecting the desired protein structure, you’re redirected to another website that host the information. In this case, it’s the Protein Data Bank in Europe (PDBe). PDBe provides an archive of experimentally determined 3D structures for biological marcomolecules. Here, we can see the 3D structure, the molecular structure, the various domains within the protein, structure analysis, and more.
- http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000206172;r=16:176680-177522
- http://www.uniprot.org/uniprot/P69905#sequences Now, let’s say you wanted to look into a desired protein sequence. When clicking the external link provided from the search page, you are redirected to the UniProt (Universal Protein Resource) page. UniProt provides a comprehensive catalog of a vast array of information on proteins as seen under “Display.” This includes it’s function, subcellular location, pathologies related to it, the various interactions that it undergoes, structure (such as the locations of helixes, turns, beta strands), the protein’s amino acid sequence, and much more.