Biomedical Engineering Reference
In-Depth Information
Sequence Visualization
Working with strings that represent nucleotide sequences is like programming in machine code.
Although it's humanly possible to program a computer with strings of 0s and 1s, it's an arduous,
error-prone, time-consuming process that doesn't lend itself to efficiency or easy maintenance and
one that requires extensive program documentation. A step up from machine code is Assembly
language, which allows programmers to use mnemonics such as "CLR" to clear a buffer and "ADD" to
add two values. However, the programmer is still forced to think in terms of low-level CPU
instructions. As a result, the programmer is constantly switching between a high-level problem such
as how to best rotate a molecule in 3D space and a low-level problem, such as whether to use
integer or floating-point math in the rotation algorithm.
Further up the programming hierarchy are languages such as C++, BASIC, and HTML that insulate
programmers from the underlying computational hardware infrastructure and allow them to work at a
level nearer the application purpose. Higher still are the flow diagrams or storyboards—maps of
sorts—that provide a graphic overview of the application that can be understood and critiqued by non-
programmers. Returning to nucleotide sequence work, the parallel to these storyboards are gene
maps—high-level graphic representations of where specific sequences reside on a chromosome.
Sequence Maps
When it comes to visualizing nucleotide sequences, the obvious organizational metaphors are the
amino acids, proteins, chromosome segments, and genes. Just as flow diagrams can be used to
provide content and a high-level description of how the various components of a program are
organized and function, gene maps provide a high-level view of relative and absolute gene and
nucleotide sequence location. The quintessential gene mapping application is NCBI's Web-based Map
Viewer, shown in
Figure 5-3
.
Figure 5-3. Map Viewer. NCBI's Map Viewer program integrates physical
and genetic map information for specific sequences, proteins, and genes.
This view shows the position of the gene associated with type 2
neurofibromatosis, located on chromosome 22.
