Model Answer

AR 7181
M. SC. (Second Semester) Examination, 2013
ZOOLOGY
Paper: LZT203
(Histology and histochemistry and bioinformatics)

Section A: Multiple Choice questions (Tick the appropriate answer)

(10 X 2)

(1)

Mordant used in naturally ripened hematoxylin is:

(c) i and ii are correct

(2)

Coagulant fixative is:

(b) Alcohol

(3)

The PAS techniques is based up on the reactivity of Schiff reagent with:

(a) Free aldehyde group of carbohydrate

(4)

Alcian blue technique gives:

(c) Red colour to nuclei

(5)

Filipen method for free cholesterol was given by:

(b) Kurth and Vaughan, 1980

(6)

Calcium lipase method for triglyceride gives:

(a) Brown colour

(7)

CPU means:
(c) Central Processing Unit

(8)

It is one of the Operating System

(c) UNIX

(9)

Environmental genomics means

(d) Database of ecosystem and biodiversity

(10)

The Neighbour-Joining Method mean

(a) Is a distance clustering method for constructing an evolutionary tree

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Q 2:

Descriptive type (Answer any four question within 200 words)

(10 X4)

Question no 2:How HCHO, Chromium salt, Hg Salt, and alcohol fixes proteins during fixation?
(2+2+2+2+2)
Answer:
Formaldehyde (HCHO):
Formaldehyde is a non-coagulant and additive fixative. Formaldehyde, as 4% buffered
formaldehyde (10% buffered formalin), is the most widely used universal fixative.It is a gas with
a very pungent odour, soluble in water to a maximum extent of 40% by weight. HCHO requires
a relatively short fixation time and used for long-term storage as it produces no deleterious
effects on tissue morphology with nuclear and cytoplasmic detail.
Formaldehyde form cross-links between proteins, creating a gel, thus retaining cellular
constituents in their in vivo relationships to each other. Soluble proteins are fixed to structural
proteins and rendered insoluble. Cross-links are formed between protein molecules and about 4060% the reaction occur with basic amino acid lysine. Other groups such as imino, amido,
peptide, guanidyl, hydroxyl, carboxyl, SH and aromatic rings are also involved in cross linking.
HCHO also react with nuclear protein and nucleic acid. It penetrates between nucleic acid and
protein, and stabilizes the nucleic acid-Protein shell. Formalin does not precipitate proteins.
Chromium Salt:
Widely used chromium salt fixatives are chromium trioxide (CrO3) and potassium dichromate
(K2Cr2O7). CrO3is a coagulant and additive fixativethat acts as a strong oxidizer
agent,whereasK2Cr2O7is a non-coagulant and additive fixative.
CrO3: The penetration rate of CrO3 is slow.Chromium salt forms complexes with water, which
combine with reactive groups of adjacent protein chains to bring about a cross-linking effect. It is
a powerful coagulant of albumin and many other proteins including nucleoprotein.
K2Cr2O7: The penetration rate is well. Potassium dichromate is a good cytoplasmic fixer and a
recommended for nucleoproteins. It gradually converts egg white more viscous and eventually
transform it into a weak gel.
Mercuric (Hg) Salt:
Mercuric chloride or corrosive sublimate (HgCl2) is acoagulant and additive fixative. It
penetrates rapidly and precipitates all proteins, reacting with a number of amino acid residues
including thiol, amino, imidazole, phosphate and hydroxyl groups. HgCl2stabilize only protein
molecule and have special affinity towards sulphur group like SH. If a small quantity of Hg salt
is added to protein containing SH group, it will react with SH group in reference to any other
group. The stability of the mercury and sulphur bond is greater than any other.
RSH + HgCl2

RS.HgCl + H++Cl-

RS.HgCl + RSH

(RS)2Hg + H++Cl-

Many such links could be formed between protein chain and many chain could be bound
together in a single polymeric form.

Osmium tetroxide(OsO4):
Osmium tetroxideis most commonly used metallic ion in fixation. It is non-coagulant and
additive fixative. Osmium tetroxide is known to form cross-links with proteins.The reactive sites
include- sulfhydryl, disulfide, phenolic, hydroxyl, carboxyl, amide and heterocyclic group. While
reacting with protein the reagent act at the two end of a double bond and a product of reaction is
a compound with two adjacent group of a diol reaction.Osmium tetroxide is capable of joining of
molecule together.Osmium tetroxide can form a link between two ring compounds by joining
with both of them, but extra supply of fixative is needed for this reaction. The amino acid
tryptophan and hystidine react strongly.

Alcohol:
Methanol and ethanol are only two alcohols that are used as fixative. Methanol is closely related
in structure to water and it competes almost as effectively as the latter for hydrogen bonds.
Ethanol is also closely related in structure and both replace water molecules in the tissues,
unbound as well as bound, during fixation. They are coagulant and non-additive fixative. They
are colorless and miscible with water in all proportion.
Alteration of the structure of proteins brought about by methanol and ethanol is primarily due to
disruption of the hydrophobic bonds which contribute to the maintenance of the tertiary structure
of proteins. Hydrogen bonds appear to be more stable in methanol and ethanol than in water so
that while affecting the tertiary structure of proteins, these alcohols may preserve their secondary
structure.
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Question no 3:
How natural and artificial hematoxylin are formed? Explain composition and preparation with
one suitable example of each. (4+3+3)
Answer:
The hematoxylin component stains the cell nuclei blue-black, with good intranuclear detail.It is
extracted from the heartwood (logwood) of the free Haematoxyloncampechianum that
originated in Mexican state of Campeche. The hematoxylin is extracted from logwood with hot
water, and then precipitated out from the aqueous solution using urea.Hematoxylin itself is not a
stain, its a colorless solid. The major oxidization product is hematein,a natural dye that is
responsible for color properties.Hematein can be produced from hematoxylin in two ways:

Natural hematoxylin is produced due to the natural oxidation(ripening) by giving exposure to

light and air. This is slow process, sometime taking as long as 3-4 months, but the resultant
solution seems to retain its staining ability for a long time. Ehrlichs and
Delafieldshematoxylin solutions are examples of naturally ripened hematoxylins.

Artificial hematoxylinis produced artificiallyby the use of certain chemical for oxidation such
as sodium iodate(Mayers hematoxylin) or mercuric oxide (Harriss hematoxylin). The use of
chemical oxidizing agents converts the hematoxylin to hematein almost instantaneously, so these
hemotoxylin solutions are ready foruse immediately after preparation. They have a shorter useful
life than the naturally oxidized hematoxylins, probably because the continuing oxidation process
in air and light eventually destroys much of the hematein.
Hematein is anionic dye,having a poor affinity for tissue, a nuclear stain without the presence but
stain of a mordant. The most useful mordant for hematoxylin are salts of aluminum, iron, and
tungsten.The mordant/ metal cationconfer a net positive charge to the dye mordant complex and
enable it to bind to anionic tissue sites such as nuclear chromatin. The type of tissue components
strained and their final color. The mordant is aluminum usually in the form of potassium alum
(aluminum potassium sulfate) or ammonium alum (aluminum ammonium sulfate). All stain the
nuclei red color, which is converted to the familiar blue-black when the section is washed in a
week alkali solution.

Composition and preparation of natural hematoxylin

(a) Ehrlichhematoxylin:
This is a naturally ripening alum hematoxylin which takes about two months to ripen. The
ripening time can be shortened somewhat by placing the unstoppered bottle in a warm sunny
place. The ripening time is shorter in summer than winter. Erlichshematoxylin is an excellent
nuclear stain, also stains mucins including the nucopolysaccharides of cartilage.
Preparation of solution
Hemetoxylin
Absolute alcohol
Glycerin
Distilled water
Glacial acetic acid
Potassium alum

2g
100ml
100ml
100ml
10 ml
15g approx

The hematoxylin is dissolved in the alcohol, and the other chemicals are added. Glycerin is
added to slow the oxidation process and prolong the hematoxylin shelf line. Natural ripening in
sunlight takes about two months.

(b) Delafield hematoxylin:It is a naturally ripened alum hematoxylin.

Preparation of solution
Hematoxylin
Saturated aqueous ammonium alum (15g/100ml)
Glycerin

125ml
400 ml
100ml

The hematoxylin is dissolved in25ml of alcohol, and the added to the alum solution. This
mixture is allowed to stand in light and air for 5 days, then filtered, and to it are added the
glycerin and a further 100ml of 95% alcohol. The stain is allowed to stand exposed to light and
air for about 3-4 months.
Composition and preparation of natural hematoxylin
(a) Mayer hematoxylin: This alum hematoxylin is chemically ripened with sodium iodate.
Preparation of solution
Hematoxylin
Distilled water
Potassium or ammonium alum
Sodium iodate
Citric acid
Choral hydrate SLR
Choral hydrate AR

1g
1000ml
50g
0.2g
1g
50g
30g

The hematoxylin, potassium alum, and sodium iodate are dissolved in the distilled water by
warming and stirring, or by allowing to stand at room temperature overnight. The chloral hydrate
and citric acid are added, and the mixture is boiled for 5 minutes, then cooled and filtered
(b) Harriss hematoxylin :Harriss was traditionally chemically ripened with mercuric
oxide.
Preparation of solution
Hematoxylin
Absolute alcohol
Potassium alum
Distilled water
Mercuric oxide
Sodium iodate
Glacial acetic acid

2.5g
25ml
50g
500ml
1.25g
0.5g
20ml

The hematoxylin is dissolved in absolute alcohol and is then added to the alum, which has
previously been dissolve in the warm distilled water. The mixture is rapidly brought to the boil
and the mercuric oxide is then slowly and carefully added. When the solution is cold, the acetic
acid is added, and the stain is ready for immediate use.

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Question no 4: Define the preparation and mechanism of Periodic acid Schiff technique? (10)
Answer:
The PAS technique is the most versatile and widely used technique for the demonstration of
carbohydrates and glycoconjugates. The first histochemical use of this technique was by
Mcmanus (1946) for the demonstration of mucin. After that PAS techniques was used for other
carbohydrate containing molecule such as glycogen and certain glycoproteins. PAS techniques
are helpful for differentiation of tumors through the detection of mucin or glycogen.

Mechanism of PAS technique:

The PAS technique is based upon the reactivity of free aldehyde group within carbohydrates with
the Schiff reagent to form a bright red magenta end product. The initial step in the PAS
techniques is the oxidation of hydroxyl group attached to adjacent carbon atoms with in the
carbohydrate.The result is the formation of two free aldehyde groups and the cleavage of the
adjoining carbon to carbon bond. The oxidation of the 1,2 glycols to form adjacent aldehydes is
produced by treatment of the sections with a dilute solution of periodic acid (HIO4). About 0.5
1.0 % solution of periodic acid is used for 5-10 minutes. The intensity of the color that develops
following reaction with Schiff reagent is dependent upon the tissue concentration of reactive
glycol structures. Monosaccharaides that lack 1,2 glycol or contain hydroxyl groups that are
involved in an ester or glycosidic linkage are not susceptible to periodic acid oxidation and hence
cannot be detected with the PAS technique. Reactive monosaccharaides include most of the
neutral sugars such as mannose, fucose, galactose, glucoseand sialic acids. The neutral sugars
and sialic acids are found in significant concentration in glycogen, epithelial mucins, and various
glycoproteins. Schiff react with the free aldehyde generated from 1,2-glycol groups in periodic
acid treated- carbohydrates. The initial monosaccharide schiff reagent conjugate is a colorless
reaction intermediate. The loosely bound sulfonate of central carbon is removed in a subsequent
aqueous rinse. The reestablishment of the quinoid structure of the triaryl methane molecule
results in the development of deep red/ magenta coloration in the site of the carbohydrate-Schiff
reagent complex.

Preparation of reagent for Periodic acid Schiff technique:

Schiff reagent is prepared from basic fuschin. Dissolve 1 g of basic fuschin and 1.9 g of sodium
metabisulfite (Na2S2O5) in 100 ml of 0.15 N hydrochloric acid (HCl). Shake the solution at
intervals or on a mechanical shaker for 2 hours. The solution should be clear and yellow to light
brown in colour. Add 500 mg of activated charcoal and shake for 1 to 2 minutes. Filter the
solution. The filtered solution should be clear and colorless. If the solution is yellow, repeat the
charcoal decolonization using a fresh lot of activated charcoal. Store at 4C.
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Question no 5:Give an account on histochemical methods used for disulfide and sulfhydral
linkages. (10)
Answer:
Disulfide and sulfhydral linkages are found in the amino acids cysteine and methionine and in
the derived amino acid cysteine. The disulfide linkage occurs between two sulfur atoms (-S-S-)
and the sulfhydral grouping is found between a sulfur atom and a hydrogen atom (-S-H). The
sulfhydral group is produced by reaction of a disulfide link. To confirm that a positive reaction is
due to presenceof sulfhydral group, duplicate sections are always treated with saturated aqueous
mercuric chloride solution for 24 hours at room temperature prior to the technique.Performic
acid-alcian blue method was generally adopted for histochemical studies used for disulfide and
sulfhydral.
Performic acid-alcian blue method:
This method was given by Adams and Sloper, 1955.
Fixation and section:
Neutral buffered formalin, formaldehyde vapor is used for fixation. Paraffin, freez-dried and
froxencryostst sections are processed for histochemical identification of disulfide and sulfhydral
linkages.
Solutions:
Performic acid solution
Concentrated formic acid

40 ml

30% hydrogen peroxide

4.0 ml

Concentrated sulfuric acid

0.5 ml

Alcian blue solution

Alcian blue

1.0 g

Concentrated sulfuric acid

2.7 ml

Distilled water

47.2 ml

Method:
1.
2.
3.
4.
5.
6.
7.
8.
9.

Take section to water, blot to remove surplus water.

Emerge sections in performic acid solution for about 5 minutes.
Wash well in tap water for atleast 10 minutes.
Dry to 60C oven until just dry.
Rinse in tap water.
Stain in alcian blue solution at room temperature. For about 1 hours.
Wash in running tap water.
Counter stain with neutral red for nuclei staining.
Wash in tap water, dehydrate through alcohols, clear in xylene, and mount.
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Question no 6:
What is Sudan black B method? Differentiate Bromine Sudan black and
Bromine acetone Sudan black methods? (5+5)
Answer:
Lipids specially oily and greasy hydrophobic lipids have an affinity for sudan dyes. Sudan B is
the most sensitive and versatile dye that was introduced by Lison and Dangelie, 1935. About
70% ethanol is an adequate solvent. Sudan black B stains phospholipid as well as neutral fat.
Procedure of Sudan Black B method for fats and phospholipids
Fixation and sections:
Cryostat sections post fixed in formal calcium, short fixed frozen sections, unfixed cryostat
sections
Method:
1. Rinse sections in 70% ethanol.
2. Stain for upto 2 hours in saturated Sudan black b in 70% ethanol.
3. Rinse in 70% ethanol to remove excess surface dye, and wash in tap water.
4. Counterstain nuclei with Kernechtrot for 2-5 minutes.
5. Wash well and mount in glycerin jelly.

Results:
The standard Sudan black B procedure stains unsaturated esters and triglycerides blue-black.
Some phospholipids appear gray and those in myelin exhibit a bronze dichroism in polarized
light.Bromination enhances the reaction of these lipids and in addition stains lecithin, free fatty
acids, and free cholesterol.
Bromine Sudan black method for lipids: It was given by Bayliss and Adams, 1972.
Method
1. Mount sections onto the slides and allow to dry.
2. Immerse sections in 2.5% aqueous bromine for 30 minutes at room temperature, inside a
fume hood
3. Wash in water and treat with 0.5% sodium metabisulphite for 1 minute to remove excess
bromine.
4. Wash thoroughly in distilled water and treat, together with an unbrominated section, for
the standard Sudan black B method.
Bromine acetone Sudan black method for phospholipids: It was given by Bayliss High, 1981
Method
1. Treat sections with 2.5% aqueous bromine for 30 minutes at room temperature inside a
fume cupboard.
2. Wash well and remove excess bromine with 0.5% sodium metabisulphite for 1 minute.
3. Wash thoroughly and allow slides to dry.
4. Extract neutral lipids with anhydrous acetone for 20 minutes at 48oC.
5. Proceed with the standard Sudan black B method.
Results
Phospholipids
Sphingomyelin

gray
bronze in polarized light
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Question no 7: Draw a block diagram to explain the basic organization of computer system and
explain the functions of various units. (10)
Answer:
Most of the computers available today on the market are the so called von Neumann computers,
simply because their main building parts, CPU or processor, memory, and I/O are interconnected
the way von Neumann suggested. Figure 1.1 presents the basic building blocks of todays
computers; even though there are many variations, and the level at which these blocks can be
found is different, sometimes at the system level, other times at board level or even at chip level,
their meaning is yet the same.

 CPU is the core of the computer: all computation is done here and the whole
System is controlled by the CPU
The program and the data for the program are stored in the memory
I/O provides means of entering the program and data into the system. It also allows the user to
get the results of computation. Computation and control in CPU The computation part of the
CPU, called the data-path, consists of the following units:
ALU (Arithmetic and Logic Unit) which performs arithmetic and logic operations;
Registers to hold variables or intermediary results of computation, as well as special purpose
registers;
The interconnections between them (internal buses).
The data-path contains most of the CPU's state; this is the information the programmer has to
save when the program is suspended; restoring this information makes the computation look like
nothing had happened. The state includes the user visible general purpose registers, as well as the
Program Counter (PC: it contains the address of the next instruction to be executed), the Interrupt
Address Register (IAR: contains the address of the instruction being suspended), and a Program
Status Register (PSR: this usually holds the status flags for the machine, like condition codes,
masks for interrupts, etc.). With a few exceptions (like PC or IAR) there is no rule to indicate if
some special signification register must be kept in the general purpose area (also called the
register-file), or in a specially dedicated register. Should the stack-pointer or the frame-pointer,
for instance, have special registers with dedicated hardware to help them perform the functions
they are meant to, or they can simply reside in the register file? On one hand a structure without
special features is cleaner, in the sense that it is easier to design and debug; on the other hand
there are strong reasons to have special purpose registers, and the most important is efficiency.
The PC, for example, is a special register, because it has a special function which could be
otherwise impossible to perform: its content has to be incremented in each instruction with some
value; special hardware helps optimizing this function; as a matter of fact, in many designs, the
program counter is closer to a counter than to a simple D-tIt is also to be mentioned that some
special registers can be accessed only by specialized instructions (in the case of PC only by
jumps, call/return, branches, with all their variants), thus providing superior protection against
accidental alteration, as compared with a general purpose register. It can be long argued about
what functions the ALU should perform, and there are at least two aspects to be considered:
encoding: the operation to be performed in the CPU is somewhere encoded in the instruction,
using a number of bits; with n bits one can specify 2n different binary configurations, i.e. that
many ALU operations. If n is too small then it will be impossible to accommodate the minimum
number of functions the ALU should perform; if the designer is too greedy then fewer bits will
remain available to encode other information in the instruction (as for instance, where are the
operands to be used, etc.), not to mention the explosive increase in the ALU's complexity. For
the time being, three or four bits seem to be enough as control lines for the ALU

 Functionality: which is the best set of operations to implement, while keeping the design at
reasonable dimensions, and, in the mean time without impairing the programmer's ability to
implement any function from the basic set of functions we provide type register. Specialized
hardware also means that some function as the technology allowed moving to wider data paths
(16, 32, 64 and even larger in the future), it has become also possible to specify more complex
instruction formats: more explicit operands, more registers, larger offsets, etc. It is the moment to
observe that newer CPU generations are faster due to:
Faster clock rate (lower Tck); while the technology features decreased more transistors fit on
the same surface and they may operate at higher speed;
Lower IC: it takes fewer instructions to perform an integer instruction on 32-bit integers, if the
data-path is 32-bit wide as compared with an 8-bit data-path;
Lower CPI: with a more involved hardware it is possible to make large transfers (read/store
from/to memory in a single clock cycle, instead of several ones as it was the case with narrower
data-path CPUs.
Figure 2.3 presents a typical modern CPU, connected to memory. The CPU uses three buses
(Op1, Op2 and Dest). The two operands are placed on the two buses, Op1, and Op2, an operation
is performed, and the result gets on the Dest bus to be stored in any register connected to the bus.
MAR is the Memory Address Register which holds the memory address during an instruction
fetch on a load/store operation;
MDR is the Memory Data Register, used to hold the data to be written into the memory during
a store or to temporarily hold the data during a load;
Temp is a temporary register used for internal manipulation of data.
Figure 2.3 also assumes that the only way from a register to another is through ALU, therefore
ALU must be able to, as one of its functions; pass one operand from input to output. 2.3
Instruction cycle obviously there are at least two steps in the cycle of an instruction: fetch (i.e.
the instruction is brought into CPU, more precisely into IR) and execute. At a closer look several
sub steps can be seen:
1. Instruction fetch step: MAR PC IR M [MAR]
The content of PC is transferred into MAR; then the instruction at address MAR is brought into
IR.
2. Instruction decodes / register fetch step:

Decoding the instruction is the step when the control decides what should be done next; if the
instruction has a fixed fields format, then the contents of registers specified in the instruction can
be read into A and B at the same time with the decoding. It is also in this phase that PC has to be
updated; how much is to be added to the PC in order to get the new PC (i.e. the address of next
instruction to be executed)? Various factors are to be considered, like instruction width,
byte/word addressable memory, memory alignment.
3. Execution
In the case of an arithmetic logic operation whose operands are in registers the operation is
performed. If the instruction is a load/store, then the address has to be computed and only then
the operation can be performed. In the case of a branch/jump operation the target address has to
be computed and, for a conditional branch/jump, PC may be updated or not depending on the
flag (condition) being tested. The execution step could be further divided into specific substeps
for each instruction or class of instructions.

Bio-informatics involves fully the concepts of biotechnology, biochemistry and biology on the
system with large databases. So these are the concepts and operations which can be understood
and be performed by only biology background student and no other technical student as he dont
know
anything
about
biologically
oriented
terms.
And today the demand for this course is very high and it is going on increasing. Here there is less
competition for you. So if you perform well during the course you will have a bright future.
When compared to other M.Sc. courses, the course for this will be a little bit high.
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Question no 8: What is the scope of bioinformatics? Why is it a multidisciplinary field? (10)

Answer:
Bioinformatics career in is increasingly attracting the youngsters in India today. The scope of
bioinformatics is in areas like database design and maintenance, sequence assembly, proteomics,
clinical pharmacologist, sequence analysis, informatics developer and bio-analytics. Excellent
job opportunities are available in Biotech and Pharmaceutical companies in India. Indian
companies like Wipro, Reliance, Satyam, TCS and companies like Accelrys and IBM Life
Sciences Pubgene, Silicon Genetics and Tessella offer good employments to the bioinformatics

candidates. Due to increasing demand of bioinformatics candidates, a career in bioinformatics

offer good prospects.
Bioinformatics is a multi-disciplinary subject, with research questions taken from biology,
medicine, pharmacology and agricultural studies. In bioinformatics research, theoretical models,
algorithms and methods are developed for the computational modeling of complex biological
systems. Computer science and mathematics from the theoretical foundations for a major part of
bioinformatics, using methods from sub disciplines including discrete mathematics, theoretical
computer science, logic, artificial intelligence, information theory, probability theory,
mathematical statistics, data base design, programming, optimization theory, analysis, geometry,
simulation methods and visualization paradigms. In addition, scientific knowledge from a
multitude of other disciplines, among which can be found automatic control, numerical analysis,
computational science and linguistics, is used and augmented. By bridging the gaps between
these disciplines, bioinformatics makes it possible for biological research to make the transition
from an area low in data intensity, to one which is highly data-intense. To date, this research has
resulted in such progress as the mapping of the human genome, projects in functional and
comparative genomics, and new methods for drug development. Bioinformatics is constantly
opening up new possibilities for scientific research within the life sciences. At the same time,
research in biology continuously contributes new types of problems which the informatics
community has not previously encountered, helping to drive these areas forward as well.
Bioinformatics encompasses development and application of information science for gathering,
storage, processing and analysis of the large amounts of heterogeneous biological, medical and
pharmacological data which are produced in modern biology. These data which are to be
processed can, for example, be the results of large-scale projects for mapping of genomes,
transcriptomes, proteomes and metabolomes, but can also come from follow-up projects which
strive to utilize the information from the earlier infra-structure related projects to study the
functions of biological systems. Bioinformatics contributes to the progress of a large number of
research areas within the life sciences. There are many examples of the importance of
bioinformatics research to, for instance, the construction of the large databases. These databases
have made it possible to systematically store and search biologically relevant information among
the enormous amounts of raw data generated within the genome projects; and further within the
development of theory, algorithms and software for the identification of functional elements such
as genes, regulatory sequences and three-dimensional protein structure from one-dimensional
DNA sequence data. Moreover, this research drives the development of methods for identifying
and elucidating function of genetic networks for the regulation of traits which are of interest in
medical, evolutionary, agricultural and general biological research. By contributing to the
development of better methods for data management within the biological sciences, it will
become possible to construct more realistic models of biological and physiological systems by
making use of and bringing together knowledge which has been attained within a wide range of
biological disciplines.
Bioinformatics or computational biology refers to an emerging, interdisciplinary subject in
which computer technology, including software, hardware and algorithms, are applied to solving
problems arising in biology. It is the convergence of biology and computer science to store,
retrieve and analyze data. However, the field of Bioinformatics encompasses much more than
this simple definition. Data, in Bioinformatics, pertains to nucleotide sequences and protein

sequences. Bioinformatics does involve biology and computer science, but it also involves
mathematics and statistics. Most of the mathematics and statistics are hidden in the computer
science aspect of Bioinformatics.
The mathematics involved mainly deals with algorithmsa stepwise method for solving a
problem. A statistical aspect of Bioinformatics involves the e-value: the expectation value which
is aspect of Bioinformatics.
The mathematics involved mainly deals with algorithmsa stepwise method for solving a
problem. A statistical aspect of Bioinformatics involves the e-value: the expectation value which
is assessment of the statistical significance of the score. Also, the e-value is a determination of
how a match is or how much chance is involved. Therefore, it is better to get a low e-value to
have good results.
Bioinformatics is a multi-disciplinary subject. Though only about a decade old, it has become
very important for the growth of biosciences, biotechnology, and the economic prosperity of
nations. Three well-defined divisions
of Bioinformatics may be considered:
a) Molecular Bioinformatics,
b) Cellular and sub cellular Bioinformatics,
c) Organismic and community Bioinformatics.
Out of these three areas, most Bioinformatics scientists and workers practice molecular
Bioinformatics. The other two areas are more recent and are being developed. In the next 5-10
years, cellular and sub cellular Bioinformatics that will include metabolic pathways, epigenetic,
and Neuro-Bioinformatic on one hand and Bioinformatics of species diversity, behavior,
evolution and the effect of pollutants on higher as well as lower species, on the other will occupy
the main stage.
The potential of Bioinformatics in the identification of useful genes leading to the development
of new gene products, drug discovery and drug development has lead to a paradigm shift in
biology and biotechnology-these fields are becoming more and more computationally intensive.
The new paradigm, now emerging, is that all genes will be known in the new sense of being
resident in databases available electronically, and the starting point of biological investigation
will be theoretical and a scientist will begin with a theoretical conjecture and only then turning to
follow or test the hypothesis. With a much deeper understanding of the biological processes at
the molecular level, the Bioinformatics scientists have developed new techniques to analyze
genes on an industrial scale resulting in a new area of science known as genomics.
Many companies were formed during the 1990s to carry out research on genomics and
Bioinformatics, such as Gene Logic, Paradigm Genetics Inc., and GeneFormatics. In 1998, two
organizations were formed that are important to genomics and Bioinformatics. The first was the
Swiss Institute of Bioinformatics. The second, established by Craig Venter, was Celera.
Three major progressions for Bioinformatics occurred in 1988. The most publicized event, which

began in 1988, was the Human Genome Initiative, to sequence the human genome. Another
advancement that year was the foundation of the National Center of Biotechnology and
Information (NCBI) at the National Cancer Institute. A final step in 1988 was the publication of
the FASTA algorithm, which is a fast approximation of the Smith-Waterman algorithm. As a
result of the Human Genome Project and other initiatives, biomolecular data accumulate at an
accelerating rate. For example, the Protein Information Resource (PIR) database, maintained at
the National Biomedical Research Foundation of Georgetown University Medical Center and
accessible at, now contains sequences. It is therefore essential to have effective tools for
processing these data. Data processing in this context includes classifying and aligning
sequences; detecting similarities, ding protein-coding regions in DNA sequences, and predicting
molecular structure and function.
Focus of software engineering in Bioinformatics
The focus of software engineering research has been shifted from system oriented tools to u s
solving problems arising in biology. Among them, BLAST-Basic Local Alignment Search Tool
and FASTA are two most eminent tools, both being freely accessible. Using local alignment
algorithms, they try to end the best alignment between a query sequence and every sequence in a
database. There are many executions of FASTA located on the World Wide Web. The primary
site for FASTA is William Pearsons Web site at the University of Virginia. Besides the FASTA
website at the University of Virginia, other groups have developed their own FASTA interface.
The interface at European Bioinformatics Institutes Web site http://www.ebi.ac.uk/fasta3/ is one
such example.
Bioinformatics and biotechnology interaction
There is difference between bioinformatician and biotechnologist. Bioinformatician actually
helps biotechnologist. Say a drug is proposed to be designed. Problem identification of a target
protein for curing tuberculosis pathogen:
1) Bioinformatician will test and predict 3-D structure of protein with all possible variations.
2) Predict a drug molecule which will inactivate this and give full structure.
Transfer all these data to biotechnologist who will validate the target through biology and
chemistry experiments and finally approve the drug. Thus there should be intimate and seamless
interaction between software capabilities and biology lab.
It has now been universally recognized that Bioinformatics is the key to the new grand data
intensive molecular biology that will take us into the 21st century. Ser-oriented tools for problem
solving. Software tools in Bioinformatics, for example, are targeted towards

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