Download - Journal of Cell and Molecular Biology - Haliç Üniversitesi

Journal of Cell and Molecular Biology 7(2) & 8(1): 75-77, 2010 Software Review
Haliç University, Printed in Turkey.
http://jcmb.halic.edu.tr
UCSC: Genome Browser for genomic sequences
Authors: UCSC Genome Bioinformatics Group led by David Haussler and Jim Kent,
Center for Biomolecular Science & Engineering, University of California
License: Free for academic, non-profit, and personal use. A license is required for
commercial use.
Genome browser at a glance
Genome Browser is a tool for collecting all relevant
genomic sequence data in one site and provides
rapid, reliable, and simultaneous display of any
requested portion of genomes at any scale in a
graphical design. The UCSC Genome Browser
resource contains the reference (or official) public
DNA sequences and working draft assemblies for
human and a large collection of other genomes.
There are a number of tools within this site that
provides access to the sequences themselves, and
many other useful genome features to add context
to the genomic information. Researchers can use
this site to find genes and gene predictions,
expression information, SNPs and variations, crossspecies
comparative data, and many more.
Moreover, the UCSC 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.
It also provides a portal to the ENCODE project.
UCSC genome browser contribution to
research
Molecular biologists use UCSC genome browser
modules during their original research tools such
"Genome Browser", "Gene Sorter", 'Blat", "Table
Browser", "VisiGene" and "Genome Graphs" all of
which allow the user to navigate, sort, blast,
visualize and analyzes genomic data for reliable
annotation.
Moreover, researchers can learn more about
the object (e.g., known genes, conservation, or
SNPs, etc.) via researching by simply position the
mouse over information line and click, then a new
web page will appear with important details and
information. The Page Index box usually includes
sequences, microarray data, mRNA secondary
structure, protein domain structure, homologues in
other species, gene ontology descriptions, mRNA
descriptions and pathways, etc. This wealth of
information is more than enough for a molecular
biologist as a start point for genomic research.
Colours language in UCSC genome browser
Colors have important meanings in UCSC genome
browser. For instance, the Black color in gene track
indicates a protein data bank (PDB) structure entry
for this genome fragment. Dark blue indicates
NCBI-reviewed sequence, while light blue
corresponds to provisional sequences. In addition,
SNP types are also color-coded. More information
about any specific color representation and
annotation or descriptive information can be
obtained by clicking the hyperlink of the track.
Advantages and disadvantages of UCSC
genome browser
Advantages
- UCSC Genome Browser is very easy to use and
free of charge online.
- UCSC uses the same interface and display for
each of the species listed.
- In addition, UCSC can run on (almost) any
computer that has access to internet and can
return the results online or by e-mail.
- The Genome Viewer page provides several
options to make changes
- Text search strategy can be used by typing in
gene name, gene symbol, or ID, etc.
- "Automatic Zoom" and "Recenter Action" are
handy features to automatically re-center the
image where you click