WHAT IS BIOINFORMATICS?

by JOANNEFOX

Bioinformatics involves the integration of computers, software tools, and

databases in an effort to address biological questions. Bioinformatics
approaches are often used for major initiatives that generate large data
sets. Two important large-scale activities that use bioinformatics are
genomics and proteomics. Genomics refers to the analysis of genomes.
A genome can be thought of as the complete set of DNA sequences that
codes for the hereditary material that is passed on from generation to
generation. These DNA sequences include all of the genes (the
functional and physical unit of heredity passed from parent to offspring)
and transcripts (the RNA copies that are the initial step in decoding the
genetic information) included within the genome. Thus, genomics refers
to the sequencing and analysis of all of these genomic entities, including
genes and transcripts, in an organism. Proteomics, on the other hand,
refers to the analysis of the complete set of proteins or proteome. In
addition to genomics and proteomics, there are many more areas of
biology where bioinformatics is being applied (i.e., metabolomics,
transcriptomics). Each of these important areas in bioinformatics aims to
understand complex biological systems.

Many scientists today refer to the next wave in bioinformatics as systems

biology, an approach to tackle new and complex biological questions.
Systems biology involves the integration of genomics, proteomics, and
bioinformatics information to create a whole system view of a biological
entity.
Figure 1. The Wheel of Biological Understanding. System biology strives
to understand all aspects of an organism and its environment through
the combination of a variety of scientific fields.

For instance, how a signaling pathway works in a cell can be addressed

through systems biology. The genes involved in the pathway, how they
interact, and how modifications change the outcomes downstream, can
all be modeled using systems biology. Any system where the information
can be represented digitally offers a potential application for
bioinformatics. Thus bioinformatics can be applied from single cells to
whole ecosystems. By understanding the complete “parts lists” in a
genome, scientists are gaining a better understanding of complex
biological systems. Understanding the interactions that occur between all
of these parts in a genome or proteome represents the next level of
complexity in the system. Through these approaches, bioinformatics has
the potential to offer key insights into our understanding and modeling of
how specific human diseases or healthy states manifest themselves.

The beginning of bioinformatics can be traced back to Margaret Dayhoff

in 1968 and her collection of protein sequences known as the Atlas of
Protein Sequence and Structure[1]. One of the early significant
experiments in bioinformatics was the application of a sequence
similarity searching program to the identification of the origins of a viral
gene[2]. In this study, scientists used one of the first sequence similarity
searching computer programs (called FASTP), to determine that the
contents of v-sis, a cancer-causing viral sequence, were most similar to
the well-characterized cellular PDGF gene. This surprising result
provided important mechanistic insights for biologists working on how
this viral sequence causes cancer[3]. From this first initial application of
computers to biology, the field of bioinformatics has exploded. The
growth of bioinformatics is parallel to the development of DNA
sequencing technology. In the same way that the development of the
microscope in the late 1600’s revolutionized biological sciences by
allowing Anton Van Leeuwenhoek to look at cells for the first time, DNA
sequencing technology has revolutionized the field of bioinformatics. The
rapid growth of bioinformatics can be illustrated by the growth of DNA
sequences contained in the public repository of nucleotide sequences
called GenBank.

Figure 2. The Use of Computers to Process Biological Information. The

wealth of genome sequencing information has required the design of
software and the use of computers to process this information.

Genome sequencing projects have become the flagships of many

bioinformatics initiatives. The human genome sequencing project is an
example of a successful genome sequencing project but many other
genomes have also been sequenced and are being sequenced. In fact,
the first genomes to be sequenced were of viruses (i.e., the phage MS2)
and bacteria, with the genome of Haemophilus influenzae Rd being the
first genome of a free living organism to be deposited into the public
sequence databanks[4]. This accomplishment was received with less
fanfare than the completion of the human genome but it is becoming
clear that the sequencing of other genomes is an important step for
bioinformatics today. However, genome sequence by itself has limited
information. To interpret genomic information, comparative analysis of
sequences needs to be done and an important reagent for these
analyses are the publicly accessible sequence databases. Without the
databases of sequences (such as GenBank), in which biologists have
captured information about their sequence of interest, much of the rich
information obtained from genome sequencing projects would not be
available.

The same way developments in microscopy foreshadowed discoveries

in cell biology, new discoveries in information technology and molecular
biology are foreshadowing discoveries in bioinformatics. In fact, an
important part of the field of bioinformatics is the development of new
technology that enables the science of bioinformatics to proceed at a
very fast pace. On the computer side, the Internet, new software
developments, new algorithms, and the development of computer cluster
technology has enabled bioinformatics to make great leaps in terms of
the amount of data which can be efficiently analyzed. On the laboratory
side, new technologies and methods such as DNA sequencing, serial
analysis of gene expression (SAGE), microarrays, and new mass
spectrometry chemistries have developed at an equally blistering pace
enabling scientists to produce data for analyses at an incredible rate.
Bioinformatics provides both the platform technologies that enable
scientists to deal with the large amounts of data produced through
genomics and proteomics initiatives as well as the approach to interpret
these data. In many ways, bioinformatics provides the tools for applying
scientific method to large-scale data and should be seen as a scientific
approach for asking many new and different types of biological
questions.
 Figure 3. Potential Types of Bioinformatic Data. Computer based
databases of biological information enables scientist to generate all sorts
of data, from generating protein sequence and predicting protein
domains to even producing 3D structures of proteins.

The word bioinformatics has become a very popular “buzz” word in

science. Many scientists find bioinformatics exciting because it holds the
potential to dive into a whole new world of uncharted territory.
Bioinformatics is a new science and a new way of thinking that could
potentially lead to many relevant biological discoveries. Although
technology enables bioinformatics, bioinformatics is still very much about
biology. Biological questions drive all bioinformatics experiments.
Important biological questions can be addressed by bioinformatics and
include understanding the genotype-phenotype connection for human
disease, understanding structure to function relationships for proteins,
and understanding biological networks. Bioinformaticians often find that
the reagents necessary to answer these interesting biological questions
do not exist. Thus, a large part of a bioinformatician’s job is building tools
and technologies as part of the process of asking the question. For
many, bioinformatics is very popular because scientists can apply both
their biology and computer skills to developing reagents for
bioinformatics research. Many scientists are finding that bioinformatics is
an exciting new territory of scientific questioning with great potential to
benefit human health and society.

The future of bioinformatics is integration. For example, integration of a

wide variety of data sources such as clinical and genomic data will allow
us to use disease symptoms to predict genetic mutations and vice versa.
The integration of GIS data, such as maps, weather systems, with crop
health and genotype data, will allow us to predict successful outcomes of
agriculture experiments. Another future area of research in
bioinformatics is large-scale comparative genomics. For example, the
development of tools that can do 10-way comparisons of genomes will
push forward the discovery rate in this field of bioinformatics. Along
these lines, the modeling and visualization of full networks of complex
systems could be used in the future to predict how the system (or cell)
reacts, to a drug, for example. A technical set of challenges faces
bioinformatics and is being addressed by faster computers, technological
advances in disk storage space, and increased bandwidth, but by far
one of the biggest hurdles facing bioinformatics today, is the small
number of researchers in the field. This is changing as bioinformatics
moves to the forefront of research but this lag in expertise has lead to
real gaps in the knowledge of bioinformatics in the research community.
Finally, a key research question for the future of bioinformatics will be
how to computationally compare complex biological observations, such
as gene expression patterns and protein networks. Bioinformatics is
about converting biological observations to a model that a computer will
understand. This is a very challenging task since biology can be very
complex. This problem of how to digitize phenotypic data such as
behavior, electrocardiograms, and crop health into a computer readable
form offers exciting challenges for future bioinformaticians.
(Abdurakhmonov, 2016)

Abdurakhmonov, I., 2016. Bioinformatics: Basics, Development, and Future. Bioinformatics - Updated

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