Submitted by: Hamza Hameed Khan

Roll no: 0029-BH-BIO-T-19

Semester: 7th Summer
Submitted to: Dr. Ishtiaq
Subject: Bioinformatics I Assignment
 Table of Content
Introduction:..................................................................................3
Ensembl tools:................................................................................3
Ensembl Genome Browser:.............................................................3
Ensembl Variation:.........................................................................4
Ensembl Compara:.........................................................................5
Ensembl Regulation:......................................................................6
Ensembl BioMart:..........................................................................6
Ensembl REST API:..........................................................................7
Ensembl Perl API:...........................................................................8
Ensembl R API:...............................................................................8
Ensembl Python API:......................................................................9
Ensembl tools:..............................................................................10
References:..................................................................................11
 Utilizations and Applications of Ensembl

Introduction:
Ensembl is a widely used bioinformatics resource that provides a comprehensive and
integrated view of genomic data for various organisms. The ensembl project was launched
in 1999 by the european bioinformatics institute (ebi) and the wellcome trust sanger
institute, with the goal of providing a stable, accurate, and user-friendly platform for the
annotation, analysis, and visualization of genomic data. Ensembl has since become one of
the most widely used bioinformatics resources in the world, with over one billion page
views per year.
Ensembl provides a variety of tools and resources for genomic data analysis, including the
ensembl genome browser, ensembl variation, ensembl compara, ensembl regulation,
ensembl biomart, ensembl rest api, ensembl perl api, ensembl r api, ensembl python api,
and ensembl tools. These applications and resources are used by researchers,
bioinformaticians, and clinicians to study the genetic and genomic basis of human diseases,
as well as to understand the evolution and function of different organisms.

Figure 1: Ensembl Database Logo

Ensembl tools:
There are a total of 10 factors functioning together to provide maximum user interface.
1. Ensembl Genome Browser
2. Ensembl Variation
3. Ensembl Compara
4. Ensembl Regulation
5. Ensembl BioMart
6. Ensembl REST API
7. Ensembl Perl API
8. Ensembl R API
9. Ensembl Python API
 10. Ensembl Tools

Ensembl Genome Browser:

The ensembl genome browser is the primary application of the ensembl platform and is
widely used by researchers to access and analyze genomic data from a wide range of
organisms. The genome browser provides a user-friendly interface that allows users to
navigate and explore genomic data, including gene annotation, variation data, and
comparative genomics. The genome browser also includes a variety of tools and features
that allow users to perform advanced analysis and visualization of genomic data.
One of the main features of the ensembl genome browser is the ability to view and explore
gene annotation data. Users can view detailed information about genes, including their
location, exon-intron structure, and functional domains. Additionally, users can access
information about gene expression, protein-coding regions, and non-coding rnas.
The ensembl genome browser also provides a variety of tools for exploring genetic variation
data, including single nucleotide polymorphisms (snps), insertions, deletions, and structural
variants. Users can view this data in the context of the genome and can also perform
genome-wide association studies (gwas) and population genetics analyses.
The ensembl genome browser also provides a comprehensive set of tools for comparative
genomics. Users can compare the genomes of different organisms, including phylogenetic
analysis, gene orthology, and gene family information. This allows researchers to identify
conserved regions of the genome and to study the evolution of different organisms.
In addition to these features, the ensembl genome browser also provides a variety of tools
for functional genomics, including the ability to view and explore regulatory regions,
transcription factor binding sites, and histone modifications. This allows researchers to
study the regulation of gene expression and to identify potential drug targets.
Overall, the ensembl genome browser is a powerful tool for researchers in a wide range of
fields, including comparative genomics, population genetics, functional genomics, and
translational medicine. It provides a comprehensive and integrated view of genomic data
that enables researchers to make new discoveries and to advance our understanding of the
genome.

Ensembl Variation:
Ensembl variation is one of the key applications of ensembl, which provides a wide range of
tools and features for exploring genetic variation data. This includes data on single
nucleotide polymorphisms (snps), insertions, deletions, and structural variants, among
others. Ensembl variation is widely used by researchers in a variety of fields, including
population genetics, functional genomics, and translational medicine.
One of the key features of ensembl variation is its ability to provide a comprehensive view
of genetic variation data across different organisms. This includes data on genetic variation
in humans, mice, rats, zebrafish, and fruit flies, among others. Additionally, ensembl
variation also provides data on genetic variation in other organisms that are of interest to
researchers, such as plants and bacteria.
Another key feature of ensembl variation is its ability to provide a wide range of tools for
exploring and analyzing genetic variation data. This includes tools for performing genome-
wide association studies (gwas), population genetics, and functional genomics. These tools
allow researchers to identify the genetic variants that are associated with specific diseases
or traits, as well as to understand the functional consequences of these variants.
Ensembl variation also provides a variety of visualization tools that allow users to explore
and analyze genetic variation data in a user-friendly and interactive way. This includes tools
for visualizing genetic variation data in the context of the genome, as well as tools for
visualizing genetic variation data in the context of specific genes or regions.
Ensembl variation is also integrated with other ensembl applications, such as ensembl
genome browser, ensembl compara, and ensembl regulation, which allows users to explore
genetic variation data in the context of genomic data, comparative genomics, and gene
regulation. This provides a powerful and integrated view of genetic variation data that is
essential for understanding the functional consequences of genetic variation and its role in
disease and evolution.
Overall, ensembl variation is an essential tool for researchers in a variety of fields, providing
a comprehensive and integrated view of genetic variation data and a wide range of tools for
exploring and analyzing this data. This enables researchers to gain new insights into the
genetic basis of disease and evolution, and to identify new therapeutic targets for treating
genetic disorders.

Ensembl Compara:
Ensembl compara is a powerful application that allows users to compare the genomes of
different organisms, including phylogenetic analysis, gene orthology, and gene family
information. Ensembl compara provides a wide range of tools and features that allow users
to compare the genomes of different organisms, including phylogenetic analysis, gene
orthology, and gene family information. The main goal of ensembl compara is to provide
researchers with a comprehensive and integrated view of comparative genomics data,
which can be used to understand the evolution and functional relationships of genes and
genomes across different organisms.
One of the main features of ensembl compara is its ability to perform phylogenetic analysis,
which allows researchers to infer the evolutionary relationships between different
organisms based on the similarities and differences in their genomes. Ensembl compara also
provides a wide range of tools for gene orthology, which allows users to identify genes in
different organisms that have evolved from a common ancestor. This is an important tool
for understanding the functional relationships of genes across different organisms, and it
can be used to identify conserved functional domains and motifs in genes.
Ensembl compara also provides a wide range of tools for gene family analysis, which allows
researchers to identify groups of genes that have evolved from a common ancestor. Gene
families are groups of genes that have evolved from a common ancestor, and they can be
used to understand the functional relationships of genes across different organisms.
Ensembl compara provides a wide range of tools for gene family analysis, including gene
tree construction, gene tree reconciliation, and gene tree visualization.
Ensembl compara also provides a wide range of tools for functional genomics, which allows
researchers to understand the functional relationships of genes across different organisms.
Functional genomics is the study of the function of genes and genomes, and ensembl
compara provides a wide range of tools for functional genomics, including gene ontology,
gene expression, and gene regulation. Ensembl compara also provides a wide range of tools
for population genetics, which allows researchers to understand the genetic variation and
evolution of different populations.
Ensembl compara is a powerful application that allows researchers to understand the
evolution and functional relationships of genes and genomes across different organisms.
Ensembl compara provides a wide range of tools and features that allow users to compare
the genomes of different organisms, including phylogenetic analysis, gene orthology, and
gene family information. Ensembl compara is an important resource for researchers working
in the fields of comparative genomics, functional genomics, population genetics, and
evolutionary biology.

Ensembl Regulation:
Ensembl regulation is an application of ensembl that allows users to explore the regulation
of gene expression. It includes data on transcription factor binding sites, histone
modifications, and chromatin structure. This application is particularly useful for researchers
studying gene regulation and its role in various biological processes, such as development
and disease.
One of the key features of ensembl regulation is the ability to view transcription factor
binding sites and histone modifications in the context of the genome. This allows
researchers to easily identify potential regulatory regions and understand the role they play
in gene expression. Additionally, ensembl regulation provides data on chromatin structure,
which can be used to identify potential enhancers and silencers.
Ensembl regulation also includes data on epigenetic modifications, such as dna methylation
and histone modifications, which can play a role in gene expression. This data can be used
to identify potential regulatory regions and understand how they are involved in gene
expression.
Ensembl regulation also provides tools for functional genomics, such as gene ontology (go)
term enrichment analysis and gene set analysis. These tools can be used to identify genes
that are involved in specific biological processes or pathways and understand the role of
regulatory regions in these processes.
Ensembl regulation is also integrated with other ensembl applications, such as ensembl
genome browser, ensembl variation, and ensembl compara, allowing users to easily view
and analyze data from different sources. This integration allows researchers to gain a more
comprehensive understanding of the role of gene regulation in various biological processes.
Overall, ensembl regulation provides a valuable resource for researchers studying gene
regulation and its role in various biological processes. The data and tools provided by
ensembl regulation can be used to gain new insights into the regulation of gene expression
and its role in development and disease.

Ensembl BioMart:
Ensembl biomart is a web-based platform for querying and retrieving biological data from
the ensembl database. It allows users to easily access and download large amounts of data,
including gene annotation, variation, and comparative genomics data, in a variety of
formats.
One of the main applications of ensembl biomart is in the field of functional genomics
research. Researchers can use it to identify genes associated with a particular phenotype or
disease, and to analyze patterns of gene expression across different tissue types or
conditions. Additionally, ensembl biomart can be used to help researchers understand the
evolutionary relationships between different species, by comparing their genomes and
identifying conserved regions and gene orthologs.
Ensembl biomart is also commonly used in the field of bioinformatics. It offers a simple
interface to access and retrieve large amounts of data, making it a useful tool for data
mining and analysis. Additionally, ensembl biomart can be integrated with other
bioinformatics tools and pipelines, to enable complex data analysis and visualization.
Another application of ensembl biomart is in the field of drug discovery and development.
Researchers can use it to identify potential drug targets and to understand the molecular
mechanisms of drug action. Additionally, ensembl biomart can be used to identify genetic
variations that may affect drug response or toxicity.
Ensembl biomart is also used by educators and students in the field of biology and
bioinformatics. It offers a user-friendly interface and a wide variety of data resources,
making it an excellent tool for teaching and learning about genetics and genomics.
Overall, ensembl biomart is a powerful and versatile tool that is widely used in the fields of
functional genomics, bioinformatics, drug discovery, and education. Its ability to retrieve
and analyze large amounts of biological data makes it an essential tool for researchers and
educators working in these fields.
Ensembl REST API:
The ensembl rest api is a powerful tool for accessing and manipulating genomic data. This
api allows developers to easily access and query the ensembl database, which contains a
wealth of information about genomes, genes, and variations. The api is versatile and can be
used for a wide range of applications, from bioinformatics research to data visualization and
analysis.
One of the most common uses of the ensembl rest api is for bioinformatics research.
Researchers can use the api to quickly and easily access large amounts of genomic data,
allowing them to identify patterns and correlations that may be difficult to find using other
methods. For example, researchers may use the api to identify genes that are associated
with a particular disease, or to identify genetic variations that may be linked to certain traits
or conditions.
Another popular use of the ensembl rest api is for data visualization and analysis. The api
allows developers to easily create interactive visualizations of genomic data, such as gene
expression patterns, genetic variations, and functional annotations. These visualizations can
be used to explore and understand the data in new ways, making it easier to identify
patterns and correlations that might not be apparent from raw data alone.
In addition to its use in bioinformatics research and data visualization, the ensembl rest api
can also be used for other applications such as drug discovery. The api can be used to
identify potential drug targets by searching for genes that are associated with a particular
disease, or by searching for genetic variations that may be linked to certain traits or
conditions. In this way, the ensembl rest api can help to streamline the drug discovery
process and accelerate the development of new therapies.
Overall, the ensembl rest api is a versatile and powerful tool that can be used for a wide
range of applications in bioinformatics, data visualization, and drug discovery. With its
ability to easily access and query large amounts of genomic data, the api is an essential tool
for researchers, developers, and other professionals working in these fields.

Ensembl Perl API:

The ensembl perl api is a powerful tool for bioinformatics research and analysis. It allows
developers and researchers to access and manipulate data from the ensembl database,
which contains information on genome sequences, annotations, and comparative genomics
for a wide range of organisms.
One of the main applications of the ensembl perl api is in the field of gene annotation.
Researchers can use the api to retrieve information on gene location, function, and
expression levels, as well as information on related genes and pathways. This can be useful
for identifying potential drug targets, understanding disease mechanisms, and studying the
evolution of gene function.
Another application of the ensembl perl api is in the field of comparative genomics.
Researchers can use the api to retrieve information on gene homology, synteny, and
phylogenetic relationships between different organisms. This can be useful for
understanding the evolution of genomes and identifying conserved regions that may be
important for gene regulation or disease susceptibility.
The ensembl perl api can also be used in the field of functional genomics, where researchers
can use the api to retrieve information on gene expression levels, protein-protein
interactions, and functional domains. This can be useful for identifying genes that are
differentially expressed in different tissues or conditions, and for understanding the
molecular mechanisms underlying disease.
Overall, the ensembl perl api is a valuable tool for bioinformatics research and analysis,
providing easy access to a wealth of genomic data and enabling researchers to make new
discoveries and insights into the workings of genomes.

Ensembl R API:
The ensembl r api is a powerful tool for bioinformaticians and biologists to access and
analyze genetic data. The api allows users to easily retrieve and manipulate genomic data
from the ensembl database, including gene annotation, variation data, and comparative
genomics. This makes it a valuable resource for both basic and applied research in genetics
and genomics.
One of the main applications of the ensembl r api is gene annotation. The api allows users to
easily retrieve information about genes, such as their location on the genome, their
function, and the proteins they encode. This can be useful for identifying genes that are
relevant to a particular research question or for understanding the genetic basis of a
disease.
Another important application of the ensembl r api is in the analysis of variation data. The
api allows users to easily retrieve information about genetic variations, such as snps and
indels, and to analyze their impact on gene function. This can be useful for identifying
genetic risk factors for diseases and for understanding the mechanisms by which genetic
variations affect disease susceptibility.
The ensembl r api also has applications in comparative genomics. The api allows users to
easily retrieve and compare genomic data from different species, which can be useful for
identifying evolutionary relationships and for understanding the mechanisms of genome
evolution.
Overall, the ensembl r api is a powerful tool for analyzing genetic data. It is widely used by
researchers in genetics and genomics and has many applications in both basic and applied
research. With its easy-to-use interface and extensive dataset, it is an essential tool for
anyone working in the field of genetics and genomics.
Ensembl Python API:
The ensembl python api is a powerful tool for working with genomic data in python. It
provides a simple and efficient way to access and manipulate large amounts of genomic
data, making it an ideal tool for a wide range of bioinformatics applications.
One of the most common uses of the ensembl python api is for gene annotation. The api
allows developers to easily retrieve information about genes, such as their location,
structure, and function. This information can then be used to annotate large-scale genomic
datasets, such as those generated by next-generation sequencing technologies.
Another popular use of the ensembl python api is for variant analysis. The api provides
access to a wide range of genomic variation data, including single nucleotide polymorphisms
(snps), insertions, deletions, and structural variations. This data can be used to perform
genome-wide association studies (gwas) and other forms of genetic analysis.
The ensembl python api also has applications in the field of functional genomics. The api
provides access to a wide range of functional genomic data, including gene expression data,
regulatory elements, and protein-protein interactions. This data can be used to study the
mechanisms underlying genetic diseases and to identify potential therapeutic targets.
In addition to these specific applications, the ensembl python api can also be used as a
general-purpose tool for working with genomic data. The api provides a flexible and easy-to-
use interface for performing a wide range of bioinformatics tasks, such as data visualization,
data analysis, and data management.
Overall, the ensembl python api is a valuable tool for bioinformatics researchers and
developers. Its ability to efficiently access and manipulate large amounts of genomic data
makes it an ideal tool for a wide range of applications in the field of genomics and functional
genomics.

Ensembl tools:
Ensembl tools is a set of command-line tools that are provided as part of the ensembl
bioinformatics platform. These tools allow users to perform various tasks, such as data
dump, data conversion, and data visualization. They are designed to be easy to use and are
well-documented, making them accessible to researchers, clinicians, and bioinformaticians
of all skill levels.
One of the primary applications of ensembl tools is data dump, which allows users to extract
data from the ensembl database in a variety of formats. This includes data on genes,
transcripts, exons, introns, regulatory regions, and other functional elements. Users can
choose to export data in formats such as fasta, gff3, and bed, which can be easily imported
into other software tools for further analysis. Additionally, ensembl tools provide the option
to export data in a compressed format, which can save storage space and reduce the time it
takes to download the data.
Another application of ensembl tools is data conversion, which allows users to convert data
between different formats. This can be useful for researchers who need to import data into
 their own analysis pipeline, or for clinicians who need to integrate data from different
sources. Ensembl tools provide a variety of options for data conversion, including options to
convert data from bed, gff, fasta, and other formats.
Ensembl tools also provide a number of visualization options, which allow users to view data
in a variety of ways. For example, the tools provide options for creating genome browser
tracks, which can be used to view data in the context of the genome. Users can also create
heatmaps, which can be used to visualize data on a per-gene basis. Additionally, ensembl
tools provide options to create plots, which can be used to visualize data in a graphical
format.
The ensembl tools also provide a number of options for the functional annotation of genetic
variations, including the prediction of their effects on protein structure and function, as well
as the identification of potential disease-causing variants. This can be useful for researchers
who are studying the genetic basis of diseases and for clinicians who are identifying
potential therapeutic targets.
Ensembl tools also provide a number of options for comparative genomics, which allow
users to compare genomic data from different species and identify evolutionary
relationships between them. This can be useful for the identification of conserved regions,
the prediction of gene function and the discovery of new genes. Additionally, ensembl tools
provide tools for the alignment of genomic sequences, which can be used to identify
conserved regions and study the evolution of genomic regions.
In conclusion, ensembl tools is a set of command-line tools that are provided as part of the
ensembl bioinformatics platform. They provide a wide range of options for data dump, data
conversion, data visualization, and functional annotation of genetic variations. Ensembl
tools are widely used by researchers, clinicians, and bioinformaticians in various fields,
including genetics, genomics, and biomedical research, making it a valuable resource for the
scientific community. The tools are easy to use and well-documented, making them
accessible to users of all skill levels.

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