Bioinformatics. About ENSEMBL genome browser.

1. ROLE OF ENSEMBL IN
GENOME BROWSING
PRESENTED BY: JOYDEEP PAL
STUDENT CODE: BWU/BBT/18/036
TOPIC: ROLE OF ENSEMBLE IN GENOME BROWSING
SUBJECT: GENOMICS AND PROTEOMICS (BBT602)
REG: NO: 18013000519 OF 2018-19
ROLL NO: 18010310021
DATE: 12.05.21

2.  GENOME BROWSER:
• In bioinformatics genome browser is a
graphical interface for display of
information from a biological
database for genomic data.
• Genome browsers enable researchers
to visualize and browse entire
genomes.
• A large number of genome browsers
are available, many of them free and
with database accessible online.
• Among the best known are the UCSC
genome browser, ENSEMBL genome
browser and NCBI’S genome data
viewer.

3.  WHAT IS ENSEMBL GENOME
BROWSER?
• Ensembl genome database project
is a scientific project.
• To provide a centralized resource for
geneticists, molecular biologists and
other researchers studying
the genomics of our own species
and other vertebrates and model
organisms.
• Launched in 1999 in response to
the imminent completion of the
human genome project.
• Research center: European
Bioinformatics Institute.
• Website: http://www.ensembl.org/
FIG: Ensembl
contains information
on chordate genomes,
including human,
mouse, rat, zebrafish,
panda, and takifugu.
FIG: HOME PAGE OF
ENSEMBL GENOME
BROWSER

4. WHY
ENSEMBL?
FIG: The Ensembl genome browser provides access to
organized information from the analysis of biological data.

5.  THE STEPS TO SEARCH BIOLOGICAL DATA IN ENSEMBL
DATABASE
STEP 1:
http://www.ensembl.org/
STEP 2: SELECT HUMAN AS
SPECIES
STEP 3: Write DNMT3B GENE and press Go
STEP 4:
Select 1st
DNMT3B
gene for
Human.

6.  THE STEPS TO SEARCH BIOLOGICAL DATA IN ENSEMBL
DATABASE
STEP 5: We get the info. About the DNMT3B gene
for human
STEP 6: Select gene
molecular function
(For example)
We can get the molecular
functions of the gene like,
DNA binding, protein
binding, chromatin binding
etc..

7.  SOME TOOLS OF
ENSEMBL:
1. VARIANT EFFECT PREDICTOR: Analyze our own variants and predict the functional
consequences of known and unknown variants via our variant effect predictor (VEP)
tool.
2. BIO-MART: Use this data-mining tool to export custom datasets from Ensembl.
3. ID HISTORY CONVERTER: Convert a set of Ensembl ids from a previous release into
their current equivalents.
4. POST-GWAS: UPLOAD GWAS SUMMARY STATISTICS.
Variant effect predictor
GWAS

8.  TYPES OF ENSEMBL GENOME
BROWSER:
• The types of Ensembl genome are: Ensembl
fungi, Ensembl protists, Ensembl plants,
Ensembl metazoa, Ensembl bacteria.
• Each site contains data for selected species
from their domain, chosen, for their scientific
interest. Ensembl Bacteria
Ensembl Fungi Ensembl
Protists
Ensembl Metazoa Ensembl Plants

9.  TYPES WITH EXAMPLE OF ENSEMBL GENOME
BROWSER:
Ensembl
Fungi
Ensembl
Protists
Ensembl
Plants
Ensembl
Metazoa
Ensembl
Bacteria
ENSEMBL GENOME BROWSER
YEAS
T
Plasmodiu
m
E.coli
Arabidopsi
s thaliana
Drosophila
melanogas
ter

10.  The Ensembl
project:
• “Ensembl is a joint project between
EMBL European bioinformatics
institute and the sanger institute to
develop a software system which
produces and maintains automatic
annotation on eukaryotic
genomes”.
• “The main aim of this campaign is
to encourage scientists across the
world - in academia, pharmaceutical
companies, and the biotechnology
and computer industries - to use
this free information”.
EMBL-EBI
SCIENTISTS OF
EMBL-EBI AND
SANGER
INSTITUTE

11. ACKNOWLEDGEMENT
• I WOULDLIKETOTHANKOURRESPECTEDFACULTYDR. SAYANTANGHOSHSIRFORGUIDANCEANDSUPPORTME TO
WORKIN THISKINDOFINTERESTINGTOPIC.