Image Processing Reference
In-Depth Information
complex biological problems. Despite the variety of scientific goals and data types in
these areas, several common themes have emerged from our combined work. First,
the accelerated experimental process in biology due to high-throughput technologies
is requiring that visualization tools be developed rapidly and nimbly to be relevant
to the discovery process. Second, many interesting visualization challenges now
exist around the idea of integrating very different types of data and finding complex
patterns within. And third, close collaboration with biologists is essential for devel-
oping visualization design requirements—we have found that these requirements
often require many interviews and multiple prototypes to articulate clearly.
The rest of this chapter discusses visualization in the context of comparative
genomics (Sect. 22.2 ), functional genomics (Sect. 22.3 ), and evolutionary and devel-
opmental biology (Sect. 22.4 ). In each section we will cover the common types of
biological questions and data in each of these fields, along with typical methods and
techniques for visualizing the data. We also discuss visualization challenges as well
as present case studies that highlight the biological impact of visualization tools.
22.2 Comparative Genomics
In the field of comparative genomics, scientists compare the genomes of organisms
to answer questions about evolution and how the genome encodes cellular functions.
These comparisons look for regions of similar DNA sequences which provide evi-
dence of common ancestry as well as potential shared function, giving insight into
the Tree of Life, the discovery of new genes, and the understanding of how our DNA
makes us who we are.
When studying the similarities and differences between genomes, these scien-
tists are most often looking for similar features of interests, such as genes. Finding
similar features implies a conservation relationship between the features, meaning
these features were conserved through evolution as the individual species diverged
from a common ancestor. Finding these similar features within large genomic data
sets relies on sophisticated computational algorithms. These algorithms characterize
conservation across a range of scales, from the genome down to the gene. Finding
patterns of conservation, across multiple scales, allows scientists to answer questions
like: Is there evidence of larger segments of conservation that could indicate a whole
genome duplication? What changes to a genome can account for species variation?
What segments of the genome account for the ability of a species to adapt to different
environments?
22.2.1 Data in Comparative Genomics
A genome is physically composed of multiple, distinct chromosomes. Each chro-
mosome is made up of a string of nucleotides which come in four common types
 
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