Biomedical Engineering Reference
In-Depth Information
defense and intelligence in the biological domain. Applications discussed in-
clude reasonable scenarios in (a) medical applications (e.g., in oncology, rapid
screening, among a selected set of individuals, for expressed genes characteristic
of specific cancers; see also preceding chapter 2 by Stolovitzky), (b) biological
warfare (e.g., for biological threat analysis, rapid screening of a large selected
set of personnel for possible susceptibility to natural or artificial diseases or en-
vironmental stresses, via their expressed genes), and (c) intelligence (e.g., identi-
fication of an individual, out of a large selected subpopulation, from small
portions of highly fragmented DNA).
1.3. Organization of the Chapter
In this section we have provided a brief medical science motivation for a
Biomolecular Database system, and a brief overview of the system. In §2 we
briefly discuss relevant conventional biotechnologies and briefly overview the
biomolecular computing (also known as DNA computing) field. In §3 we de-
scribe in detail our Biomolecular Database system. In that section we make use
of various relevant biomolecular computing methods, including the use of word
designs for synthetic DNA tags, execution of parallel associative search queries
on DNA databases, and the execution of logical operations using recombinant
DNA operations. In §4 we discuss a number of genomic processing applications
of Biomolecular Database systems. In §5 we conclude with a review of potential
advantages of Biomolecular Database systems.
2.
REVIEW OF BIOTECHNOLOGIES FOR GENOMICS AND THE
BIOMOLECULAR COMPUTING FIELD
2.1. Conventional Biotechnologies for Genomics
There have been considerable commercial biotechnological developments
in the last few decades, and many further increases in scale can reasonably be
expected over the next five years. For example, the DNA hybridization array
technology developed by Affymetrix Inc. (the capability is currently up to
400,000 output spots, and within 5 years a projected 1,000,000 outputs) can be
adapted for output of queries to conventional optical/electronic media. Other
biotechnology firms (e.g., Genzyme Molecular Oncology Inc.) have developed
competing biotechnologies.
2.1.1. Genomics
In the research field known as genomics , there are a number of main areas
of focus, each with somewhat different goals. These include:
1. DNA sequencing . Sequencing is the determination of the specific base
pair sequence making up the DNA. This tells us all the possible genes that a
given organism may express—its genetic makeup. In conventional bioinformat-
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