EMBL(European Molecular Biology Laboratory) Database
History
EMBL was the idea of LeóSzilárd, James Watson and John Kendrew. Their
goal was to create an International Research Centre, similar to CERN, to rival the strongly American-dominated
field of molecular biology. Kendrew
served as the first Director-general of
EMBL until 1982 and was succeeded by LennartPhilipson. From 1993 to 2005, FotisKafatos, served as director and was succeeded
by Iain Mattaj, EMBL's fourth director, from 2005 to 2018. In
January 2019, Edith Heard became the fifth director of EMBL and the first
woman to hold this position.
Research Information
Each EMBL site has a specific research
field. The EMBL-EBI is a hub for bioinformatics research
and services, developing and maintaining a large number of scientific databases
that are free of charge. At Grenoble and Hamburg, research is focused on structural biology.
The EMBL Rome site is dedicated to the
study of epigenetics and neurobiology. Scientists at EMBL Barcelona are exploring how tissues
and organs function and develop, in health and disease. At
the headquarters in Heidelberg, there are units in cell biology and biophysics, developmental biology, genome biology,
and structural and computational biology, as well as service groups
complementing the aforementioned research fields.
Many scientific breakthroughs have
been made at EMBL. The first systematic genetic analysis of embryonic
development in the fruit fly was conducted at EMBL by Christiane Nüsslein-Volhard and Eric Wieschaus, for
which they were awarded the Nobel Prize in
Physiology or Medicine in
1995. In the early 1980s, Jacques Dubochet and
his team at EMBL developed cryogenic electron microscopy for biological structures. They
were rewarded with the 2017 Nobel Prize in Chemistry.
Primary databases (also
known as data repositories) are highly organized, user-friendly gateways to the
huge amount of biological data produced by researchers around the world. The
primary databases were first developed for the storage of experimentally
determined DNA and protein sequences in the 1980s and 90s. In those times,
proteins were sequenced one amino acid at a time and DNA sequencing was in its
infancy, so repositories contained a limited number of sequences. However, with
the arrival of automatic DNA sequencing, these data banks started to grow
exponentially. Nowadays, sequence submissions are made by individual
laboratories, as well as “in bulk” by sequencing centers around the world, and
DNA submissions now greatly outnumber protein sequence submissions. Most
protein sequences found in databases are the product of conceptual translation
of the genes and genomes determined using DNA sequencing.
The GenBank format allows for the storage of
information in addition to a DNA/protein sequence. It holds much more
information than the FASTA format. Formats similar to GenBank have been
developed by ENA (EMBL format) and by DDBJ (DDBJ format).
Primary databases have developed highly
structured data file formats that enable the storage of all of these additional
data that accompany the otherwise “naked” DNA sequence encoded in a FASTA file.
The strict layout is necessary for the file to be compatible with a range of computer
programs. Each of the three primary databases have their own sequence file
format layout. However, all of them contain almost the same fields and the same
information, making them interchangeable. It is worth noting that there are
many more file formats that have been customized to serve specific purposes.
Those we are going to discuss here store additional information related to DNA
and protein sequences. For simplicity, we are going to present the GenBank
sequence file format only, but we will discuss the EMBL format in the following
activities.
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