WHAT IS A GENOME BROWSER

GENOME BROWSERS
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 INTRODUCTION
 Genome browsers allow researchers to navigate the genome in an analogous way to
navigating the internet. Genome browsers have been created to allow the simultaneous
display of multiple annotations within a graphical interface. In addition, they provide the
ability to search for markers and sequences, to extract annotations for specific regions or
for the whole genome and to act as a central starting point for genomic research. The
number and variety of annotations has increased dramatically, enabling a detailed view of
many aspects of the genome.
 GENOME BROWSER
 Genome browsers can be described and compared with respect to presentation, content
and functionality. Presentation refers to how the data are displayed in a graphical form
and the overall structure of the website. Content refers to what data is accessible, such as
particular genome sequences and annotations for a specific genome. Functionality refers
to tools available for mining the genome sequence and annotations, such as sequence and
text searches and data extraction. The UCSC, Ensembl and NCBI genome browsers aim
to present genomic data in a manner that will facilitate research, but they do so in
different ways.


 UCSC GENOME BROWSER
 The UCSC Genome Browser is an on-line genome browser hosted by the University of
California, Santa Cruz (UCSC), and UC Santa Cruz opened in 1965 with 650 students.
During the 2016-2017 academic years, 16,328 undergraduate and 1,735 graduate students
were enrolled.
 It is a popular Web-based tool for quickly displaying a requested portion of a genome at
any scale, accompanied by a series of aligned annotation tracks, open source platform
designed for the fast, scalable display of sequence alignments and annotations landscaped
against a vast collection of quality reference genome assemblies.
 The University of California Santa Cruz (UCSC) Genome Bioinformatics Web site
at http://genome.ucsc.edu provides links to a variety of genome analysis tools, most
notably the UCSC Genome Browser, a graphical tool for viewing a specified region of a
genome and a collection of aligned annotation “tracks.”
 Another tool on the Web site the UCSC Table Browser supplies convenient access to the
MySql database tables underlying the Genome Browser annotations.
Presentation
 UCSC features three types of browsers: a genome browser, a gene family browser (Gene
Sorter) and a proteome browser. The genome browser is the most widely used.
https://en.wikipedia.org/wiki/Genome_browser
https://en.wikipedia.org/wiki/University_of_California,_Santa_Cruz
https://en.wikipedia.org/wiki/University_of_California,_Santa_Cruz
http://genome.ucsc.edu/


 The web page of the genome browser consists of a graphic that displays annotations for
specified genomic region surrounded by navigational buttons and links to tools. The
primary web page of the genome browser consists of a graphic that displays annotations
for some specified genomic region surrounded by navigational buttons and links to tools.
 The navigational buttons allow for zooming in and out or moving left or right along the
genomic sequence. Within the graphic, annotations also referred to as ‘tracks’ are
displayed horizontally, with the genome sequence running from left to right.
 Arrows indicate forward or reverse strand. The use of different colours and shading of
boxes highlights the properties of certain annotations, such as confidence in the
underlying data as is the case in the Known Genes track and quantitative traits, employed
by the GC Percent track to indicate differing levels of content of guanine (G) and
cytosine (C) base pairs.
 Clicking on an element within an annotation will bring up a separate ‘details’ web page
with specific information about that element and links to other databases...