EMBL-EBI

A center for excellence for biology research

Sayma Zerin 2nd year, B.S.(Hons.)Dept. of Genetic Engineering & Biotechnology

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.

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

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/

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.

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

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.

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

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: 

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:

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

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

THE END THANK YOU ANY QUESTION????

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