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A center for excellence for biology research

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

http://www.ebi.ac.uk/
5

22.01.2014
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
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
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
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
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
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
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
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.
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
USING PEPSTAT/PEPWINDOW/PEPINFO

Input of protein sequence that is to be analyzed by pepinfo/pepwindow/pepstat tool
15

22.01.2014
RESULTS FROM PEPSTAT

16

22.01.2014
RESULTS FROM PEPINFO

17

22.01.2014
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
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
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
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
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
THE END
THANK YOU
ANY QUESTION????

23

22.01.2014

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EMBL-EBI

  • 1. A center for excellence for biology research Sayma Zerin 2nd year, B.S.(Hons.) Dept. of Genetic Engineering & Biotechnology
  • 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. 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. 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
  • 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. 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. 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. 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. 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. 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. 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. 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. 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. USING PEPSTAT/PEPWINDOW/PEPINFO Input of protein sequence that is to be analyzed by pepinfo/pepwindow/pepstat tool 15 22.01.2014
  • 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. 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. 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. 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. 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. THE END THANK YOU ANY QUESTION???? 23 22.01.2014