Python Notes for mca i year students osmania university.docx
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
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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
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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
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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
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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.
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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
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11. MICROARRAY ANALYSIS
Microarray Analysis tools at the EBI are:
Expression
Profiler:
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• 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.
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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.
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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
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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.
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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.
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20. TRAINING & INDUSTRY CHANNEL
Events
at EBI
General
training
train
online
Training
programmes
phD
program
me
EICAT
2can
Industry
support
portal
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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
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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
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one-stop
station to
the
submission
tools and
documents
