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BioInformatics

AND

QUANTUMCOMPUTING
BIO INFORMATICS

Introduction:

Biology is defined as the study of living things for which biologists collect and interpret
data. Today, sophisticated laboratory technology allows us to collect data faster than we
can interpret it. We have vast volumes of DNA sequence data but how do we figure out
which parts of that DNA control the various chemical processes of life? We know the
function and structure of some proteins, but how do we determine the function of new
proteins? And how do we predict what a protein will look like, based on the knowledge
of its sequence? We understand the relatively simple code that translates DNA into
protein. But how do we find meaningful new words in the code and add them to the
DNA-protein dictionary?

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So what is ‘Bioinformatics'?

Basically, Bioinformatics is the science of using information to understand

biology. It may be broadly defined as the interface between Life Sciences and
Computational Sciences. It is a subset of the larger field of Computational
Biology that includes the application of quantitative analytical techniques in
modeling biological systems. It is a science that deals with genomics - an area of
study which looks at the DNA sequence of an organism in order to determine
what genes code for beneficial traits and which genes are involved in inherited
diseases. As biology is advancing, more and more information is generated and
scientists need a way to store and analyze it. Computers can greatly assist that
process. As a result, this new research area, which combines the study of
biotechnology and the use of computers, is emerging. It involves the use of
Internet tools, artificial intelligence and other advanced computational methods to
assist in storing and analyzing data generated from DNA sequencing.

The field of bioinformatics relies heavily on work by experts in statistical

methods and pattern recognition. Researchers (or bioinformaticians) come to it from
many fields, including mathematics, computer science, and linguistics. By providing
algorithms, databases, user interfaces, and statistical tools, bioinformatics makes it
possible to do exciting things such as compare DNA sequences and generate results that
are potentially significant. These new tools also give you the opportunity to over interpret
data and assign meaning where none really exists!

Bioinformatics is thus the study of the information content and information flow
in biological systems and processes and the application of computational and analytical
methods to biological problems. But the main goal of bioinformatics isn't developing the
most elegant algorithms or the most arcane analyses; the goal is finding out how living
things work!

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How Is Computing Changing Biology?

An organism's hereditary and functional information is stored as DNA,

RNA, and proteins, all of which are linear chains composed of smaller molecules.
These macromolecules are assembled from a fixed alphabet of well-understood
chemicals: DNA is made up of four deoxyribonucleotides (adenine, thymine,
cytosine, and guanine), RNA is made up from the four ribonucleotides (adenine,
uracil, cytosine, and guanine), and proteins are made from the 20 amino acids.
Because these macromolecules are linear chains of defined components, they can
be represented as sequences of symbols. These sequences can then be compared to
find similarities that suggest the molecules are related by form or function.

The Eye of the Fly Example:

Fruit flies (Drosophila melanogaster) have a gene called eyeless, which, if

it's knocked out (i.e., eliminated from the genome using molecular biology
methods), results in fruit flies with no eyes and hence the eyeless gene plays a role
in eye development.

Researchers have identified a human gene responsible for a condition called

aniridia. In humans, who are missing this gene or in whom the gene has mutated
stop functioning properly, the eyes develop without irises.

As little as 15 years ago, looking for similarities between eyeless and

aniridia DNA sequences would have been like looking for a needle in a haystack.
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Most scientists compared the respective gene sequences by hand-aligning them

one under the other in a word processor and looking for matches character by
character. This was very unweildy. However, in the late 1980s, fast computer
programs made it possible for pairwise comparison of biological sequences which
is the foundation of most widely used bioinformatics techniques.

How does sequence alignment work?

It's important to remember that biological sequence (DNA or protein) has

a chemical function, but when it's reduced to a single-letter code, it also functions
as a unique label, almost like a bar code. The sequence label can be applied to a
gene, its product, its function, its role in cellular metabolism, and so on. The user
searching for information related to a particular gene can then use rapid pair-wise
sequence comparison to access any information that's been linked to that sequence
label.

The most important thing about these sequence labels, though, is that they
don't just uniquely identify a particular gene; they also contain biologically
meaningful patterns that allow users to compare different labels, connect
information, and make inferences. So not only can the labels connect all the
information about one gene, they can help users connect information about genes
that are slightly or even dramatically different in sequence. So simply, every DNA
sequence could be slapped with a unique number or ID and be done with it. But
biological sequences are related by evolution, so a partial pattern match between
two sequence labels is a significant find.

Basically, it involves:

• Finding the genes in the DNA sequences of various organisms

• Developing methods to predict the structure and/or function of newly discovered

proteins and structural RNA sequences.

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• Clustering protein sequences into families of related sequences and the

development of protein models.

• Aligning similar proteins to examine evolutionary relationships.

QUANTUM COMPUTING
INTRODUCTION

BIOINFORMATICS AND QUANTUM COMPUTERS

The genomic code breaks down into thousands of individual genes. Genes tell
cells to make proteins - individual molecules each one of which has a unique chemical
mission. Proteins interact with each other to carry out thousands of functions, from
digesting your dinner to synthesizing the small molecules that form a barrier between the
inside of your cells and the outside world.

There are many ways in which computers can aid research into this. For example -

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• Collecting and processing signals detected by laboratory equipment as DNA

sequencers, CCD devices, spectrophotometers, and just about any other device
that can be connected to a computer via an analog to digital converter.

• Tracking samples and managing experiments in industrial-style laboratories

• Storing data in public databases, and more importantly, public access to the
database via sophisticated Web searches and deposition mechanisms.

• Using automatic computational methods to assign functional meaning to

uncharacterized data and to create informative links between different data
collections. For example, using automated sequence comparison searches to
identify potential genes in new genome data.

• Using known information about a system to simulate properties of the system.

Thus, with the help of computers, bioinformaticians work with data generated by
the experimental biology community and by a growing number of data factory projects
(e.g. genome sequencing projects). This data is mined to develop new hypotheses, new
models of how biological systems function, and even rules and patterns which can be
used to screen new data sets.

Let us take up two examples -

1. Information Storage in quantum computers -

As mentioned above, DNA is a molecule made from sugar, phosphate and bases
called guanine (G), cytosine (C), adenine (A), and thymine (T). The various combinations
these four bases make up the DNA in plants, animals, bacteria, yeast and fungi. An
infinite number of combinations of these bases are possible. For example you could have
AAGCT, CCAGT, TACGGT etc.

Scientists are currently trying to determine the entire DNA sequence of various
living things. By the end of this year, it has been predicted that the human genome

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sequence databases (such as GenBank and EMBL), that are already present on the net as
for all the scientists to collectively work on information, will have grown to 4 billion base
pairs! These databases have been growing at exponential rates. This deluge of
information has necessitated the careful storage, organization and indexing of sequence
information. For Example, in agricultural research, the effort to sequence the Arabidopsis
genome will require determining the sequence of a 120 - megabase sequence. Computers
can greatly assist in storing and managing all of this information.

2. Data analysis –

Results generated from DNA sequencing could identify genes, regulatory sequences and
other functions. Once the information of the DNA sequence has been determined, the
next step is to find out what these genes code for. Comparing one DNA sequence to
another amongst closely related organisms assists these processes. Computers can help
compare DNA sequences and look for homologies, or related strands of DNA. One can
also compare DNA sequences to determine how closely two different species are related
on an evolutionary scale.

What Challenges Does Biology Offer Computer Scientists?

The goal of biology, in the era of the genome projects, is to develop a

quantitative understanding of how living things are built from the genome that
encodes them. Cracking the genome code is complex. At the very simplest level,
we still have difficulty identifying unknown genes by computer analysis of
genomic sequence. Beyond the single-molecule level, the challenges are
immense. As datatypes beyond DNA, RNA, and protein sequence begin to
undergo the same kind of explosion, simply managing, accessing, and presenting
this data to users in an intelligible form is a critical task. Human-computer
interaction specialists need to work closely with academic and clinical researchers
in the biological sciences to manage such staggering amounts of data. Biological
data is very complex and interlinked. A spot on a DNA array, for instance, is
connected not only to immediate information about its intensity, but to layers of

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information about genomic location, DNA sequence, structure, function, and

more. Creating information systems that allow biologists to seamlessly follow
these links without getting lost in a sea of information is also a huge opportunity
for computer scientists. Finally, each gene in the genome isn't an independent
entity. Multiple genes interact to form biochemical pathways, which in turn feed
into other pathways. Putting genomic and biochemical data together into
quantitative and predictive models of biochemistry and physiology is the work of
bioinformaticians and computer scientists, mathematicians, and statisticians are
also a vital part of this effort.

INSIDE QUANTUM COMPUTING

It's a commonplace to observe the tremendous pace of change in the computer industry. For
many decades computers have doubled in power every year or so, and this trend looks set to
continue for at least the next decade. Given this enormous rate of change, it is perhaps
surprising to learn that all existing computers work according to essentially the same set of
principles, a set of principles enunciated by the mathematician Alan Turing in 1936, and
worked out in more detail by the mathematician John von Neumann in the 1940s. These
principles define a paradigm for computation ("classical computation") that has persisted
essentially unchanged in the decades since Turing and von Neumann, despite the enormous
technical improvements that enable far more capable devices to be produced now than was
possible in the first half of the twentieth century.

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PRINCIPLES BEHIND

Quantum computers are different. They work according to quantum mechanical principles that
transcend the notions of Turing and von Neumann. These principles expand the range of
operations that a quantum computer can perform beyond what is possible on a classical
computer, giving us a new and likely more powerful paradigm for computation. To understand
how a quantum computer operates it helps to understand the three main differences between
classical and quantum computation.
The first difference is in the fundamental units of information processed by the two types of
computers. A classical computer is built up from bits - physical systems which can be in one of
two states that we identify with "0" or "1". A quantum computer is built up from qubits,
physical systems which possess states analogous to the classical 0 or 1, but which can also be
in states intermediate between 0 and 1. These intermediate states, known as superposition
states, in some sense allow a single qubit to store much more information than is possible in
an ordinary classical bit.
The second difference between quantum and classical computers is in the range of logical
operations that may be performed within the computer. Classical computers operate according
to binary logic, using logical gates such as the AND gate which take two bits as input and
produce a bit as output. Quantum logic gates take one or more qubits as input and produce
one or more qubits as output

SPECIAL FEATURE
The third difference between quantum and classical computers is in the process of determining
the state of the computer. In a classical computer we can read out the state of all the bits in
the computer at any time. Rather strangely, in a quantum computer it is in principle
impossible to determine the exact state of the computer. That is, we can't determine exactly
which superposition state is being stored in the qubits making up the computer. Rather, we
can only obtain partial information about the state of the computer. Designing algorithms for
quantum computers is thus a delicate balance between exploiting the expanded range of
states and logical operations afforded by quantum computation and the restricted readout of
information possible in the computer.
What can quantum computers do? Unfortunately, at the moment we have a very incomplete
picture of the capabilities of quantum computers, but a few interesting facts are known. In
particular, there are a few problems that are believed (but not rigorously proved!) to be very
difficult to solve on a classical computer that should be relatively easy to solve on a quantum
computer - assuming we ever solve the hard problem of actually building such a device! Two

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interesting examples of such problems are the problem of finding the prime factors of large
numbers, and the problem of simulating quantum mechanical systems. Both these problems
are enormously important for a wide range of practical reasons, and they are believed to be
very hard to solve on classical computers, but researchers have found theoretical algorithms
for quantum computers that are vastly more efficient than the best known classical
algorithms.

Conclusion:

Biologists want to collect all of the information they can about every gene
in every genome, and from that information construct models using computational
techniques for analyzing how genes work together to build up and maintain a
living body, whether it's a bacterium or a star quarterback!

FURTHER READING
Reading is arranged roughly in increasing order of difficulty.
M. A. Nielsen, "Introduction to quantum information theory", available on the web at
http://xxx.lanl.gov/abs/quant-ph/0011064.
E. Knill and M. A. Nielsen, "Theory of quantum computation", available on the web at
http://xxx.lanl.gov/abs/quant-ph/0010057.
D. Aharonov, "Quantum computation", available on the web at http://xxx.lanl.gov/abs/quant-
ph/9812037.
A. Steane, "Quantum computing", available on the web at http://xxx.lanl.gov/abs/quant-
ph/9708022.
M. A. Nielsen and I. L. Chuang, "Quantum computation and quantum information", Cambridge
University Press, Cambridge (2000). See also http://www.squint.org/qci for an excerpt from
the first chapter and ordering information.

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