EMBL-EBI

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EMBL-EBI

  1. 1. A center for excellence for biology research Sayma Zerin 2nd year, B.S.(Hons.) Dept. of Genetic Engineering & Biotechnology
  2. 2. The European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory(EMBL). EMBL-EBI grew out of EMBL’s pioneering work to provide public biological database to research community. It is located on the Wellcome Trust Genome Campus in Hinxton, UK along with wellcome trust sanger institute.
  3. 3. HISTORY • EMBL-Nucleotide Sequence Data Library 1980 • EMBL council voted for establishing 1992 EBI. • Transfer of databases from EMBL to 1992 EBI campus. -95 • Final establishment of EBI in wellcome trust genome campus 1995 3 22.01.2014
  4. 4. MAIN SERVICES The main services the EBI offers are devided into five major sections: Distribution of data over the internet,the website and the ftp server. Processing of submission to the nucleotide and protein sequences databases Email and web based job submission Training and education Industry programme services 4 22.01.2014
  5. 5. EBI Website http://www.ebi.ac.uk/ 5 22.01.2014
  6. 6. THE CHANNELS The EBI website is divided into seven channels: The databases channel The tools channel The research channel The training channel The industry channel http://www.ebi.ac.uk/Inform ation/sitemap.html. About the EBI Help Site map 6 22.01.2014
  7. 7. DATABASE CHANNEL The database channel contains various databases categorized according . to molecule types: Biological ontologies Literature Functional genomics Neucleotides Pathway and networks Proteins- protein sequence databases, Protein function databses. Proteomic Small molecule Structure 7 22.01.2014
  8. 8. EBI: a data hub for bioinformatics in Europe Literature ebi.ac.uk/citexplore Genomes: ensembl.org Protein sequence uniprot.org DNA +RNA sequences ebi.ac.uk/ena Protein structure ebi.ac.uk/pdbe Transcriptomes e.g. ArrayExpress Small molecules ebi.ac.uk/chebi andebi.ac.uk/che mbl Protein domains, families ebi.ac.uk/interpro Protein protein interactions ebi.ac.uk/intact Pathways reactome.org Systems biomodels.net
  9. 9. ArrayExpress - for gene expression data ENA - Europe's primary comprehensive nucleotide sequence data resource. UniProt Knowledgebase - a complete annotated protein sequence database. Ensembl - Providing up to date completed metazoic genomes and the best possible automatic annotation. IntAct - Provides a freely available, open source database system and analysis tools for protein interaction data. 9 22.01.2014
  10. 10. TOOLS CHANNEL This section contains tools divided into following categories: Microarray analysis Protein functional analysis Proteomic service Structural analysis Sequence analysis Similarity and homology Tools- miscellaneous 10 22.01.2014
  11. 11. MICROARRAY ANALYSIS Microarray Analysis tools at the EBI are: Expression Profiler: 11 22.01.2014 • platform for microarray gene expression, sequence and PPI data analysis, pattern discovery
  12. 12. PROTEIN FUNCTIONAL ANALYSIS The following are the protein functional analysis tools available at the EBI. FingerPRINTScan-PRINTS Protein fingerprint searches. Inquisitor-provides a single query interface for identifying protein sequences. InterProScan-Search protein sequences against InterPro databases. Phobius-predict transmembrane topology and signal peptides. PPsearch -Protein motifs searches. Pratt-Discover patterns in unaligned proetin sequences. Radar-Protein repeat detection. 12 22.01.2014
  13. 13. PROTEOMIC SERVICES This section provides access to proteomic services offered by the EBI: DOD-(Database on Demand)-generate custom FASTA formatted sequence databases. DASTY-for visualising protein sequence feature information. UniProt DAS-allows researchers to show their research results on the UniProt reference sequence server IntEnz-The Integrated relational Enzyme database. 13 22.01.2014 PRIDE-a public data repository for proteomics data.
  14. 14. SEQUENCE ANALYSIS Some of the sequence analysing tools available at EBI are: Align-Pairwise global and local alignment tool. ClustalW2-Multiple sequence alignments. MUSCLE-MUltiple Sequence Comparison by Log-Expectation.Better average accuracy and better speed than ClustalW2 or T-Coffee Pepstats/Pepwindow/Pepinfo-EMBOSS programs for basic protein sequence analysis. T-coffee- A multiple sequence alignment program that Allows to combine results obtained with several alignment methods. Transeq-DNA sequence translation tool 14 22.01.2014
  15. 15. USING PEPSTAT/PEPWINDOW/PEPINFO Input of protein sequence that is to be analyzed by pepinfo/pepwindow/pepstat tool 15 22.01.2014
  16. 16. RESULTS FROM PEPSTAT 16 22.01.2014
  17. 17. RESULTS FROM PEPINFO 17 22.01.2014
  18. 18. SEQUENCE SIMILARITY SEARCHING Sequence Similarity Searching is a method of searching sequence databases by using alignment to a query sequence. Some of the tools are-BLAST,WU-B:AST,PSI-BLUST,FASTA. 18 22.01.2014
  19. 19. TOOLS - MISCELLANEOUS The following are the various other utilities which are available at the EBI. EMBL computational services-a collection of tools provided by EMBL to analyse DNA/protein sequences. Protein colorer-a tool for colouring your amino acid sequences. Readseq- sequence format convertion tool. 19 22.01.2014
  20. 20. TRAINING & INDUSTRY CHANNEL Events at EBI General training train online Training programmes phD program me EICAT 2can Industry support portal 20 22.01.2014 Science for school
  21. 21. ABOUT US CHANNEL The about us channel contain various section about EBI which are categorized mainly as: Mission Guidence structure Fundings News and press Jobs events 21 22.01.2014
  22. 22. DOWNLOAD & SUBMISSION Download • vast data from databases and bioinformatics software from database and tools channel Submission• ftp://ftp.ebi.ac.uk/ The main accesspoint 22 22.01.2014 one-stop station to the submission tools and documents
  23. 23. THE END THANK YOU ANY QUESTION???? 23 22.01.2014

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