discovery .

Finally, we conclude by
BIO-INFORMATICS
describing why bioinformatics has become
such a hot topic in career option. Hence
---Detecting The Future Bioinformatics is,

Abstract: “Involving computers to know the

blue print of life…”
In this paper we present a brief idea of
Bioinformatics. Firstly, we describe about role
of computers in bioinformatics, in the
identification of unknown virus. Then we
present the creation of databases of the protein
structures .Then we move to the core of the Introduction:
paper which deals with the similarity Bioinformatics, as reflected by the
searching techniques: FASTA and PSI- term has two components -‘Bio’ and
BLAST. In FASTA, we describe its ‘Informatics’ and as such primarily depicts the
application and sequence format of multiple convergence of two fields of biology and
alignments with an example, which information technology. Bioinformatics is the
determines among horse, mike whale and red application of computer technology to the
kangaroo which two species are closely management of biological information.
related. In PSI-BLAST, we Specifically, it is the science of developing
computer databases and algorithms to
facilitate and expedite biological research. The
Human Genome Project (HGP) has been the
biggest achievement of bioinformatics to date.

present the flow chat of a PSI-BLAST Other areas of bioinformatics are sequence

searching technique and an example which alignment, protein structure prediction,

answers, why pig, or in general, animal systems biology, protein-protein interactions

derived insulin can be used to treat diabetes. and virtual evolution.[SR’04]

Then we discuss the application of Computers in Bioinformatics:

bioinformatics mainly in the field of drug
 When scientists talk about virus creates an epidemic of fatal disease in
bioinformatics or “doing bioinformatics”, they humans or animals. Laboratory scientists will
mean the use of computers to store, retrieve, isolate its genetic material and determine the
analyze, predict and simulate the nature and sequence. Computer programs will take over.
properties of biological macromolecules like Viruses contain protein molecules which are
nucleic acids (e.g.: deoxyribonucleic acid, or suitable targets, for drugs that will interfere
DNA), and proteins (the product of DNA). with viral structure or function. From the viral
Computers and their networking via internet DNA sequences, computer programs will
help the biologists not only to store large derive the amino acid sequences and other
volumes of data but also to retrieve data from programs will compute the structures of these
anywhere around the world quickly. Scientists proteins and functional properties. First data
and software enthusiasts have designed banks will be screened for related proteins of
innumerable computational tools for analysis known structure. If no related protein of
of various physio-chemical and structural known structure is found, and viral protein
properties of biomolecules. These tools help appears genuinely new, the structure
biologists with difficult mathematical prediction must be done entirely ab initio.
modeling and thus save time, money and
effort. Thus, bioinformatics has ushered in the Creation of Sequence Databases:
age of ‘in silico’ biology in contrast to in vivo
and in vitro studies. Most biological databases consist of
long strings of nucleotides or amino acids.
Each sequence of nucleotides or amino acids
represents a particular gene or protein,
respectively. Sequences are represented in
shorthand, using single letter designations.
While most biological databases contain
nucleotide and protein sequence information,
there are also databases which include
taxonomic information such as the structural
and biochemical character such as Perl and
For example, imagine a crisis-
Python are often used to interface with
sometime in future-in which a new biological
 biological databases and parse output from A very common format for sequence data is
bioinformatics programs. derived from conventions of FASTA, a
program for FAST Alignment by
Similarity searching techniques: W.R.Pearson.

Theoretical scientists have derived A Sequence in FASTA format:

new and sophisticated algorithms which allow
sequences to be readily compared using  Begin with a single-line description. A
probability theories. These comparisons > must appear in the first column.
become the basis for determining gene  Subsequent lines contain the sequence,
function, developing phylogenetic one character per residue.
relationships and simulating protein models.  Use one letter codes for nucleotides or
The two popular data based similarity amino acids specified by IUB and IUPAC
searching techniques FASTA and BLASTA.  Lines can have different lengths, i.e.,
[HLC-95] Computer scripting languages such ‘ragged right’ margins.
as Perl and Python are often used to interface  Most programs will accept lower case
with biological databases. letters as amino acid codes.

PSI-BLAST:
BLAST is Basic Local Sequence Alignment
Tool. This program has variants which check
entry in the databank independently against
query sequence. This program is so commonly
used that the first encounter you have with
bioinformatics tools and biological databases
will probably be through the National Center for
Biotechnology Information's (NCBI) BLAST
web interface.
Often the databank contains close
FASTA: matches to the query sequence. Less sensitive
but faster programs are quite capable of
 identifying the close matches, and if that is what  Go back to step 2, until a cycle
is required. The method used by BLAST goes produces no change.
back, in a sense to the dot plot approach, The below is an example for a
checking for well-matching local regions. For BLAST. The following pictures show the
each entry in the database, it checks for short reason why pig, or in general, animal derived
contiguous regions that match a short insulin can be used to treat diabetes: As can be
contiguous region in the query sequence, using seen in these figures, the amino acid sequences
substation scoring matrix but allowing no gaps. of the animal insulin are very similar to the
An approach in which candidate regions of human form. Amino acids, symbolized using the
fixed length are identified initially can be made one-letter-code, which match exactly are
very fast by use of lookup tables. The PSI- displayed in the middle row marked with
BLAST was originally designed to solve that a horizontal lines. Those which do not match are
full dynamic programming methods are rather marked with vertical bars. The sequence identity
slow for complete searches in a large databank. is 94% for rabbits, 89% for pigs, and 87% for

A flowchart for PSI-BLAST: cows.

 Probe each sequence in the chosen

database independently for local regions of
similarity to the query sequence, using a
BLAST-type search but allowing gaps.
 Collect significant hits. Construct a
multiple sequence alignment table between
the query sequence and the significant local
Fig: IMAGE OF HUMAN INSULIN
matches.
 Form a profile from the multiple
PSI-BLAST, using iterated pattern
sequence alignment.
search, is much more powerful than simple pair
 Reprove the database with the profile,
wise BLAST in picking up distant relationships.
still looking only for local matches.
PSI-BLAST correctly identifies three times as
 Decide which hits are statistically
many homologues as BLAST .Therefore its
significant and retain these only.
better method for analyzing genomes.

Application of Bioinformatics:
 Companies in the business of
developing drugs, agricultural chemicals, Instead of taking a generic or over the

hybrid plants, plastics and other petroleum counter drug for a particular condition, a

derivatives, and biological approaches to patient would submit a tissue sample, such

environmental remediation, among others, are as a mouth scraping, and submit it for

developing bioinformatics divisions and analysis. A micro array would then be

looking to bioinformatics to provide new used to analyze the patient’s genome and

targets and to help replace scarce natural the appropriate compounds would be

resources. Bioinformatics can lead to prescribed.

important discoveries as well as help How will this or any

companies save time and money in the long other killer application be realized? The

run. The continuing partnership between answer lies in addressing the

Inpharmatica and Sun Microsystems is a good molecularbiology, computational and

example of how life sciences firms can meet practical business aspects of proposed

this bioinformatics challenge. developments such as custom medications.

Consider the technical challenges that
The Killer Application:
need to be successfully overcome to
“What might be a computer enabled
develop a just in time designer drug
killer application in bioinformatics?” That
system. A practical system would include:
is, what is the irresistible driving force that
 High throughput screening - The usage
differentiates from a purely academic
of affordable computer-enabled micro
endeavor? Altough there numerous
array technology to determine the patient’s
military and agricultural opportunities, one
genetic profile. The issue here is
of the most commonly cited examples of
affordability, in that micro arrays costs
the killer application are in personalized
tens of thousands of dollars.
medicine. It is depicted in the figure.
Medically relevant information
gathering- Databases on gene expression,
medical relevance of signs and symptoms transmitted as signal of some type through
and references for the patient should be a medium.
readily available. The goal is to be able to
quickly and automatically match a
When the signal is intercepted the
patient’s genetic profile.
receiver extracts the message or
Custom drug synthesis- The just in time
information from the signal, which is
synthesis of patient specific drugs, based
delivered to the destination. Shannon’s
on the patient’s medical condition and
model also provides the theoretical basis
genetic profile, presents major technical as
for data compression, which is the way to
well as social and legal hurdles. For
squeeze more information into a message
example, for just in time synthesis to be
by eliminating redundancy. Shannon’s
accepted by FDA, the pharmaceutical
model is especially relevant for developing
industry must demonstrate that custom
gene sequencing devices and evaluation
drugs can skip the clinical-trails gauntlet
techniques.
before approval.
Achieving this killer application in biotech
is highly dependent on computer Conclusion:
technology, especially in the use of Bioinformatics is first and foremost a
computers to speed the process testing- component of the biological sciences.
analysis-drug synthesis cycle.
Therefore, it is imperative to
The Shannon’s model of information appreciate the fact that to deal in
theory: bioinformatics, one must necessarily
This model of information theory understand the essentials of molecular biology
describes a communication system with on the one hand and the fundamental
five major parts: the information source, principles of computer and information
the transmitter, the medium, the receiver, technology.
and the destination. In this model the
information can be a CD_ROM containing Bioinformatics has created a great
the sequence information of the entire hullabaloo in career option. Biologists with
human gene, contains the message that is knowledge of computers, computer
 enthusiasts with their biology basics freshened  FASTA -
up, mathematics freaks with a penchant for ftp://ftp.virginia.edu/pub/fasta/
computational wizardry, biostatisticians and
physicists who can handle computers-are all
being welcomed into the big new world of
bioinformatics. One of the biggest reasons for
bioinformatics being a hot field is the old
supply and demand adage. There just are too
few people adequately trained in both biology
and computer science to solve the problems
that biologists need to have solved.
“Bioinformatics is a tool
and not an end in itself.”

References:
Books:
 [SR’04] SCIENCE REPORTER
-NOV2004
 [HLC-95] Holm.L and Sander-
Network tools for protein structure – 1995
 [BI’03] Arthur-Bioinformatics-2003

Internet resources:
 Human Genome Project and
Bioinformatics
(http://www.ornl.gov/TechResources/Human
_Genome/research/informatics.html)
 Bioinformatics journal
(http://bioinformatics.oupjournals.org/)
 BLAST -
http://ncbi.nlm.nih.gov/BLAST/