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A center for excellence for biology research
Sayma Zerin 2nd year, B.S.(Hons.)Dept. of Genetic Engineering & Biotechnology
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What is EBI?
It is located on the Wellcome Trust Genome Campus in Hinxton, UK along with wellcome trust sanger institute.
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.
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HISTORY
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1980 •EMBL-Nucleotide Sequence Data Library
1992 •EMBL council voted for establishing EBI.
1992-95 •Transfer of databases from EMBL to EBI campus.
1995 •Final establishment of EBI in wellcome trust genome campus
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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 databasesEmail and web based job submissionTraining and educationIndustry programme services
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EBI Website
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http://www.ebi.ac.uk/
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THE CHANNELS
The EBI website is divided into seven channels:The databases channelThe tools channelThe research channelThe training channelThe industry channelAbout the EBIHelp
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Site map
http://www.ebi.ac.uk/Information/sitemap.html.
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DATABASE CHANNEL
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The database channel contains various databases categorized according to molecule types:
Biological ontologiesLiteratureFunctional genomicsNeucleotidesPathway and networksProteins- protein sequence databases, Protein function databses.ProteomicSmall moleculeStructure
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EBI: a data hub for bioinformatics in EuropeLiteratureebi.ac.uk/citexplore
DNA +RNA sequencesebi.ac.uk/ena
Genomes: ensembl.org
Transcriptomese.g. ArrayExpress
Protein structureebi.ac.uk/pdbe
Protein domains, familiesebi.ac.uk/interpro
Pathways reactome.org
Systemsbiomodels.net
Small moleculesebi.ac.uk/chebi andebi.ac.uk/chembl
Protein sequenceuniprot.org
Protein protein interactionsebi.ac.uk/intact
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ENA - Europe's primary
comprehensive nucleotide sequence
data resource.UniProt Knowledgebase
- a complete annotated protein
sequence database.
ArrayExpress - for gene expression data
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.
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TOOLS CHANNEL
This section contains tools divided into following categories:
Microarray analysisProtein functional analysisProteomic serviceStructural analysisSequence analysisSimilarity and homologyTools- miscellaneous
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MICROARRAY ANALYSIS
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Microarray Analysis tools at the EBI are:
Expression Profiler:
• platform for microarray gene expression, sequence and PPI data analysis, pattern discovery
Bioconductor
• software project for the analysis and comprehension of genomic data
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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.
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PROTEOMIC SERVICESDASTY-for visualising protein sequence feature information.
DOD-(Database on Demand)-generate custom FASTA
formatted sequence databases.
IntEnz-The Integrated relational Enzyme database.
PRIDE-a public data repository for
proteomics data.
UniProt DAS-allows researchers to show their
research results on the UniProt reference sequence server
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This section provides access to proteomic services offered by the EBI:
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SEQUENCE ANALYSIS
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
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Some of the sequence analysing tools available at EBI are:
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USING PEPSTAT/PEPWINDOW/PEPINFO
Input of protein sequence that is to be analyzed by pepinfo/pepwindow/pepstat tool
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RESULTS FROM PEPSTAT
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RESULTS FROM PEPINFO
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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.
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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.
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TRAINING & INDUSTRY CHANNEL
Events at EBI
train online
phD programme
Science for school
2can support portal
EICAT
General training
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Trainingprogrammes
About industry programme
About SME forumSupportAnnual report
Industry
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ABOUT US CHANNEL
The about us channel contain various section about EBI which are categorized mainly as: MissionGuidence structureFundingsNews and pressJobsevents
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DOWNLOAD & SUBMISSION
Download• vast data from databases and
bioinformatics software from database and tools channel
The main accesspoint • ftp://ftp.ebi.ac.uk/
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Submission-
one-stop station to the submission tools and
documents
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THE END THANK YOU ANY QUESTION????
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