Lecture 9 - European Molecular Biology Laboratory (EMBL) | Bioinformatics - Botany PDF Download

 Page 1


EMBL 
Institute of Life Long Learning 0 
 
 
 
 
 
 
 
Subject : Bioinformatic  
Lesson : European Molecular Biology Laboratory (EMBL) 
Lesson Developer: Sandip Das 
Department/ College: Department of Botany, University of Delhi 
Page 2


EMBL 
Institute of Life Long Learning 0 
 
 
 
 
 
 
 
Subject : Bioinformatic  
Lesson : European Molecular Biology Laboratory (EMBL) 
Lesson Developer: Sandip Das 
Department/ College: Department of Botany, University of Delhi 
EMBL 
Institute of Life Long Learning 1 
   
 
Table of Contents Contents 
 Chapter : European Molecular Biology Laboratory  
?  Introduction 
 European Bioinformatics Institute 
? Databases at EBI 
? Nucleotide databases 
? Functional Genomics Databases 
? Protein databases 
? Structure databases 
? Sequence Analysis 
? Pairwise analysis 
? Multiple sequence alignment 
? Homology Searching 
? Summary  
? Exercises 
? Glossary 
? References  
 
 
 
 
 
 
 
 
 
 
 
Page 3


EMBL 
Institute of Life Long Learning 0 
 
 
 
 
 
 
 
Subject : Bioinformatic  
Lesson : European Molecular Biology Laboratory (EMBL) 
Lesson Developer: Sandip Das 
Department/ College: Department of Botany, University of Delhi 
EMBL 
Institute of Life Long Learning 1 
   
 
Table of Contents Contents 
 Chapter : European Molecular Biology Laboratory  
?  Introduction 
 European Bioinformatics Institute 
? Databases at EBI 
? Nucleotide databases 
? Functional Genomics Databases 
? Protein databases 
? Structure databases 
? Sequence Analysis 
? Pairwise analysis 
? Multiple sequence alignment 
? Homology Searching 
? Summary  
? Exercises 
? Glossary 
? References  
 
 
 
 
 
 
 
 
 
 
 
EMBL 
Institute of Life Long Learning 2 
 
 
 
Introduction  
Keeping with the tremendous growth in field of computational biology, a need was felt to 
establish an independent and parallel research institute that would act not just as a mirror 
housing the Genbank nucleotide resources of NCBI, but would also develop matching 
databases and analysis tools. The European Molecular Biology Laboratory (EMBL) was 
thus established in 1974 and is now supported with funding from 20 members states of the 
European Union (EU), Israel and Australia. EMBL currently operates five research institutes 
in different countries with main institute at Heidelberg, Germany. 
The five institutes of EMBL with their core research activities are (http://www.embl.org/): 
a. EMBL Heidelberg (Germany; http://www.embl.de/) 
b. EMBL Grenoble (France; http://www.embl.fr/index.php)- Structural Biology 
c. EMBL-European Bioinformatics Institute (EBI) Hinxton (UK; http://www.ebi.ac.uk/)- 
Bioinformatics 
d. EMBL Hamburg (Germany; http://www.embl-hamburg.de/index.php) Structural 
Biology 
e. EMBL Monterotondo (Italy; http://www.embl.it/index.php)- Mouse Biology 
 
The broad goals of EMBL are: 
a. Basic research in Molecular biology 
b. Training manpower i.e. students, scientist and visitors 
c. Develop new tools, technologies and methods 
d. Offer service to the research community 
e. Transfer technology to industry for commercialization 
 
Page 4


EMBL 
Institute of Life Long Learning 0 
 
 
 
 
 
 
 
Subject : Bioinformatic  
Lesson : European Molecular Biology Laboratory (EMBL) 
Lesson Developer: Sandip Das 
Department/ College: Department of Botany, University of Delhi 
EMBL 
Institute of Life Long Learning 1 
   
 
Table of Contents Contents 
 Chapter : European Molecular Biology Laboratory  
?  Introduction 
 European Bioinformatics Institute 
? Databases at EBI 
? Nucleotide databases 
? Functional Genomics Databases 
? Protein databases 
? Structure databases 
? Sequence Analysis 
? Pairwise analysis 
? Multiple sequence alignment 
? Homology Searching 
? Summary  
? Exercises 
? Glossary 
? References  
 
 
 
 
 
 
 
 
 
 
 
EMBL 
Institute of Life Long Learning 2 
 
 
 
Introduction  
Keeping with the tremendous growth in field of computational biology, a need was felt to 
establish an independent and parallel research institute that would act not just as a mirror 
housing the Genbank nucleotide resources of NCBI, but would also develop matching 
databases and analysis tools. The European Molecular Biology Laboratory (EMBL) was 
thus established in 1974 and is now supported with funding from 20 members states of the 
European Union (EU), Israel and Australia. EMBL currently operates five research institutes 
in different countries with main institute at Heidelberg, Germany. 
The five institutes of EMBL with their core research activities are (http://www.embl.org/): 
a. EMBL Heidelberg (Germany; http://www.embl.de/) 
b. EMBL Grenoble (France; http://www.embl.fr/index.php)- Structural Biology 
c. EMBL-European Bioinformatics Institute (EBI) Hinxton (UK; http://www.ebi.ac.uk/)- 
Bioinformatics 
d. EMBL Hamburg (Germany; http://www.embl-hamburg.de/index.php) Structural 
Biology 
e. EMBL Monterotondo (Italy; http://www.embl.it/index.php)- Mouse Biology 
 
The broad goals of EMBL are: 
a. Basic research in Molecular biology 
b. Training manpower i.e. students, scientist and visitors 
c. Develop new tools, technologies and methods 
d. Offer service to the research community 
e. Transfer technology to industry for commercialization 
 
EMBL 
Institute of Life Long Learning 3 
We would limit ourselves to the bioinformatics research, database and facilities of EMBL 
that is located at EMBL-EBI in the following sections. 
 
European Bioinformatics Institute (EBI) 
The European Bioinformatics Institute (EBI-EMBL) was established in 1980 as the EMBL 
Nucleotide Sequence Data Library at Heidelberg and in-fact was the world’s first public 
nucleotide database preceding NCBI by eight years (NCBI was established in 1988) with an 
objective to create database of published nucleotide sequences. Subsequently in 1992, the 
EMBL decided to establish EBI as a dedicated research cum analysis facility at the Wellcome 
Trust Genome Campus, Hinxton (UK) in close proximity to Sanger Sequencing Center.  
At present, EBI-EMBL houses databases and provides service and analysis tools for all major 
research disciplines requiring computational support. In addition, EBI is also a partner and 
coordinator for International Nucleotide Sequence Database Collaboration (INSDC; 
http://www.insdc.org) for public domain nucleotide sequence information together with 
Genbank at NCBI (www.ncbi.nim.nih.gov) and DNA databank of Japan (DDBJ; 
www.ddbj.nig.ac.jp).  
The following are the broad categories of databases at EBI-EMBL: 
a. Biological Ontologies 
b. Literature 
c. Functional Genomics or microarray 
d. Nucleotides 
e. Pathways and Networks 
f. Protein 
g. Proteomics 
h. Small Molecules 
i. Structure 
 
Page 5


EMBL 
Institute of Life Long Learning 0 
 
 
 
 
 
 
 
Subject : Bioinformatic  
Lesson : European Molecular Biology Laboratory (EMBL) 
Lesson Developer: Sandip Das 
Department/ College: Department of Botany, University of Delhi 
EMBL 
Institute of Life Long Learning 1 
   
 
Table of Contents Contents 
 Chapter : European Molecular Biology Laboratory  
?  Introduction 
 European Bioinformatics Institute 
? Databases at EBI 
? Nucleotide databases 
? Functional Genomics Databases 
? Protein databases 
? Structure databases 
? Sequence Analysis 
? Pairwise analysis 
? Multiple sequence alignment 
? Homology Searching 
? Summary  
? Exercises 
? Glossary 
? References  
 
 
 
 
 
 
 
 
 
 
 
EMBL 
Institute of Life Long Learning 2 
 
 
 
Introduction  
Keeping with the tremendous growth in field of computational biology, a need was felt to 
establish an independent and parallel research institute that would act not just as a mirror 
housing the Genbank nucleotide resources of NCBI, but would also develop matching 
databases and analysis tools. The European Molecular Biology Laboratory (EMBL) was 
thus established in 1974 and is now supported with funding from 20 members states of the 
European Union (EU), Israel and Australia. EMBL currently operates five research institutes 
in different countries with main institute at Heidelberg, Germany. 
The five institutes of EMBL with their core research activities are (http://www.embl.org/): 
a. EMBL Heidelberg (Germany; http://www.embl.de/) 
b. EMBL Grenoble (France; http://www.embl.fr/index.php)- Structural Biology 
c. EMBL-European Bioinformatics Institute (EBI) Hinxton (UK; http://www.ebi.ac.uk/)- 
Bioinformatics 
d. EMBL Hamburg (Germany; http://www.embl-hamburg.de/index.php) Structural 
Biology 
e. EMBL Monterotondo (Italy; http://www.embl.it/index.php)- Mouse Biology 
 
The broad goals of EMBL are: 
a. Basic research in Molecular biology 
b. Training manpower i.e. students, scientist and visitors 
c. Develop new tools, technologies and methods 
d. Offer service to the research community 
e. Transfer technology to industry for commercialization 
 
EMBL 
Institute of Life Long Learning 3 
We would limit ourselves to the bioinformatics research, database and facilities of EMBL 
that is located at EMBL-EBI in the following sections. 
 
European Bioinformatics Institute (EBI) 
The European Bioinformatics Institute (EBI-EMBL) was established in 1980 as the EMBL 
Nucleotide Sequence Data Library at Heidelberg and in-fact was the world’s first public 
nucleotide database preceding NCBI by eight years (NCBI was established in 1988) with an 
objective to create database of published nucleotide sequences. Subsequently in 1992, the 
EMBL decided to establish EBI as a dedicated research cum analysis facility at the Wellcome 
Trust Genome Campus, Hinxton (UK) in close proximity to Sanger Sequencing Center.  
At present, EBI-EMBL houses databases and provides service and analysis tools for all major 
research disciplines requiring computational support. In addition, EBI is also a partner and 
coordinator for International Nucleotide Sequence Database Collaboration (INSDC; 
http://www.insdc.org) for public domain nucleotide sequence information together with 
Genbank at NCBI (www.ncbi.nim.nih.gov) and DNA databank of Japan (DDBJ; 
www.ddbj.nig.ac.jp).  
The following are the broad categories of databases at EBI-EMBL: 
a. Biological Ontologies 
b. Literature 
c. Functional Genomics or microarray 
d. Nucleotides 
e. Pathways and Networks 
f. Protein 
g. Proteomics 
h. Small Molecules 
i. Structure 
 
EMBL 
Institute of Life Long Learning 4 
 
Figure: Webportal of EMBL and EBI 
Source: http://www.embl.org/ , http://www.ebi.ac.uk/ 
 
Databases at EBI 
The following section will deal with selected databases of EBI-EMBL: 
Nucleotide databases 
a. European Nucleotide Archive (ENA): ENA receives nucleotide data from a variety of 
sources, including small scale sequencing studies, sequencing centers and the INSDC (i.e. 
Genbank and DDBJ). In order to better manage the sequencing resources, ENA has been 
divided in several sub-databases such as  
? ENA-Genome - for genome sequencing data