Biology Reference
In-Depth Information
about the structure or function of proteins encoded by the clicked gene,
for example. The controls at the top of the window allow the user to
scroll along the genome or to zoom in on a particular position. One can
also move around the genome by searching for particular genes or by
typing in genomic coordinates. As such, the image is dynamically gener-
ated as the user navigates around the genome.
The UCSC Genome Browser is one of the most common ways in
which biologists interact with the genome. It is an ideal tool with which
to perform a quick check on a gene or region of interest (for instance,
to see whether it is conserved, or to see whether it is aligned with any
ESTs), or to systematically search for unidentifi ed genes using multiple
sources of information (for instance, by comparing computational pre-
dictions and conservation data). For example, a researcher might wish
to know what genes lie in the fi rst 500,000 base pairs of human chro-
mosome 1. This can be done by searching the region “chr1:0-500000”
for UCSC “knowngenes.” The browser can then be used to examine
whether particular genes are conserved in other vertebrates or to fi nd
the locations of SNPs, alignments with ESTs or GenBank mRNA, and a
large amount of other information that associates particular genes with
gene products, diseases, microarray data, gene ontology information,
and metabolic pathways.
40
The presentation and organization of these
data are visual—the correspondence between different gene predictions
and between the organization and structure of genes in different or-
ganisms can be understood by visual comparison down the screen (see
fi gure 6.4). The display has been described as follows:
Gene structure is shown in these tracks with fi lled blocks rep-
resenting exons; thick blocks are in the coding sequence (CDS)
and thin blocks represent untranslated regions (UTRs). The
lines connecting the blocks are introns. The direction of the ar-
rowheads on the lines or the blocks show the strand on which
the element resides.
41
Elsewhere, colors are used to represent different sorts of codons as well
as regions of high or low conservation.
The pictorial space generated from the database creates what Durbin
and Thierry-Mieg call a “dense navigable network” that can be explored
by pointing and clicking. Tools like the UCSC Genome Browser have
generated a visual lexicon for thinking and talking about genomes. The
genome has become a “map” on which the user can “navigate” around
or “zoom” in. One of the advantages of AceDB was considered to be
