Genome browser (GB)

What are genome browser?

Genome browser is a graphical interface for users to browse, search,
retrieve and analyze genomic sequence and annotation data.

Introduction:
The initial sequence generated by the human genome project together with
the draft genome sequence of several model organisms, including the house
mouse (Mus musculus), fruit fly (Drosophila melanogaster), nematode
(Caenorhabditis elegan), baker’s yeast (Saccharomyces cerevisiae), Gram-
negative bacterium (Escherichia coli) and thale cress (Arabidopsis thaliana),
completed at the beginning of this millennium create a paradigm shift
within biological research, as predicted by Gilbert in the early 1990s.
• With the rapid development of next-generation sequencing
technologies, hundreds of eukaryotic and thousands of prokaryotic
genomes have been sequenced.
• All the sequence data as well as the annotations generated in the
genome databases and are publicly available through web portals such
as the NCBI genome portal (http://www.ncbi.nlm.nih.gov/genome/)
and the EBI genome database website (
http://www.ebi.ac.uk/Databases/genomes.html).
Types of GB
• In general, genome browser can be divided into web-based browsers
and stand-alone applications.

• Web-based genome browsers which are useful in promoting

biological research due to their data quality, flexible accessibility and
high performance
• First, dedicated organizations often collect and integrate high-quality
annotation data into web-based genome browsers, providing
plentiful up-to-date information for the community.
• Second, users can access them anywhere with a standard web
browser, avoiding any additional effort of setting up local
environment for application installation and data preparation.
• Third, web-based genome browsers are usually installed on high
performance servers and can support more complex and larger scale
data types and applications.
Ensembl
• Ensembl genome database project is a scientific project at the
European Bioinformatics Institute, which was launched in 1999 in
response to the imminent completion of the Human Genome Project.
• Ensembl (http://www.ensembl.org/) is a bioinformatics project to
organize biological information around the sequences of large
genomes.
• It is a comprehensive source of stable automatic annotation of
individual genomes, and of the synteny and orthology relationships
between them.
• The Ensembl project produces genome databases for vertebrates and
other eukaryotic species, and makes this information freely available
online.
• Ensembl aims to provide a centralized resource for geneticists,
molecular biologists and other researchers studying the genomes of
our own species and other vertebrates and model organisms.
• Ensembl is one of several well known genome browsers for the
retrieval of genomic information.
• Similar databases and browsers are found at NCBI and the University
of California, Santa Cruz (UCSC).
• Ensembl provides a genome browser that acts as a single point of access
to annotated genomes for mainly vertebrate species.
• Information about genes, transcripts and further annotation can be
retrieved at the genome, gene and protein level. This includes
information on protein domains, genetic variation, homology, syntenic
regions and regulatory elements.
• Ensembl imports genome sequences from consortia which keeps us
consistent with many other bioinformatics projects. Each species in
Ensembl has its own home page, where you can find out who provided
the genome sequence and which version of the genome assembly is
represented.
• The human genome consists of three billion base pairs, which code for
approximately 20,000–25,000 genes.
• However the genome alone is of little use, unless the locations and
relationships of individual genes can be identified.
• One option is manual annotation, whereby a team of scientists tries to
locate genes using experimental data from scientific journals and
public databases.
• However this is a slow, painstaking task. The alternative, known as
automated annotation, is to use the power of computers to do the
complex pattern matching of protein to DNA.
• In the Ensembl project, sequence data are fed into the gene annotation
system (a collection of software "pipelines" written in Perl) which
creates a set of predicted gene locations and saves them in
a MySQL database for subsequent analysis and display.
• Ensembl makes these data freely accessible to the world research
community.
• All the data and code produced by the Ensembl project is available to
download, and there is also a publicly accessible database server
allowing remote access.
• In addition, the Ensembl website provides computer-generated visual
displays of much of the data.
• Over time the project has expanded to include additional species
(including key model organisms such as mouse, fruitfly and zebrafish)
as well as a wider range of genomic data, including genetic
variations and regulatory features.
• Since April 2009, a sister project, Ensembl Genomes, has extended the
scope of Ensembl into invertebrate metazoa, plants, fungi, bacteria,
and protists, whilst the original project continues to focus on
vertebrates.
Displaying genomic data

• Central to the Ensembl concept is the ability to automatically generate

graphical views of the alignment of genes and other genomic data
against a reference genome.
• These are shown as data tracks, and individual tracks can be turned on
and off, allowing the user to customize the display to suit their
research interests.
• The interface also enables the user to zoom in to a region or move
along the genome in either direction.
• Other displays show data at varying levels of resolution, from
whole karyotypes down to text-based representations of DNA and amino
acid sequences, or present other types of display such as trees of similar
genes (homologues) across a range of species.
• The graphics are complemented by tabular displays, and in many cases data
can be exported directly from the page in a variety of standard file formats
such as FASTA.
• Externally produced data can also be added to the display by uploading a
suitable file in one of the supported formats, such as BAM, BED, or PSL.
• Graphics are generated using a suite of custom Perl modules based on GD,
the standard Perl graphics display library.
• In addition to its website, Ensembl provides a REST API and a Perl API (Application
Programming Interface) that models biological objects such as genes and proteins, allowing
simple scripts to be written to retrieve data of interest.
• The same API is used internally by the web interface to display the data. It is divided in
sections like the core API, the compara API (for comparative genomics data), the variation
API (for accessing SNPs, SNVs, CNVs..), and the functional genomics API (to access
regulatory data).
• The Ensembl website provides extensive information on how to install and use the API.
• This software can be used to access the public MySQL database, avoiding the need to
download enormous datasets. The users could even choose to retrieve data from the MySQL
with direct SQL queries, but this requires an extensive knowledge of the current database
schema.
• Large datasets can be retrieved using the BioMart data-mining tool. It provides a web
interface for downloading datasets using complex queries.
• Last, there is an FTP server which can be used to download entire MySQL databases as well
some selected data sets in other formats.
• http://ensemblgenomes.org/
How to search Ensembl?
Search www.ensembl.org using:
•a gene name (for example, BRCA2) (Figure 4)
•an identifier from an external database, such as UniProt accession number or
a PDBe ID
•a disease name (for example, coronary heart disease)
•a variant ID (for example, rs1223)
•a location – a genomic region (for example, rat X:100000..200000)
•a Gene Ontology (GO) term

Most search results will take you to the appropriate Ensembl view through a results page. If you search using a location you
will be directed straight to the location tab (this tab provides a view of a region of a genome).
• A wealth of biological data can be viewed, downloaded and compared
such as:
• genes
• conserved sequences across species
• sequence variation
• sequences implicated in gene regulation
• As well as performing genomic annotation, Ensembl also brings
together information from multiple resources, using the genome as a
base for this annotation.
 Why Ensembl?

The Ensembl genome browser provides access

to organized information from the analysis of
biological data.
• The vast amount of information that comes with annotating a genomic
sequence demands a way of organizing and accessing that information
(Figure).
• This need is met by Ensembl – a genome browser providing free access
to the complete sequences of higher and model organisms.
• Biological databases are an important resource for the life sciences
community.
• Keeping up-to-date with the hundreds of databases supporting molecular
biology and related fields is a daunting and time-consuming task.
• Integrating this information into one access point is a necessity.
• Genome browsers and their underlying databases act as single entry
points to data from multiple projects and genomic analyses, such as
genes and proteins, sequence variation, comparative genomics and
motifs involved in gene regulation.
• Ensembl and Ensembl Genomes are major projects integrating and
displaying genome annotation for multiple species.