The sequence of biomolecules contain
interesting information in and of itself.
A protein sequence can be compared to other
protein sequences to establish its evolutionary
relationship to other proteins and protein families.
Collection, storage and
Biological Database as a collection of
data that is structured, searchable,
updated periodically, and crossreferenced
Collection, storage and maintenance
a method for solving complex problems by
breaking them down into simpler sub
Molecular sequence data are at the heart of
Under 35 ye No conception after one
year of unprotected
Over 35 ye
No conception after 6
months of unprotected
Stress on Relationships
Stress on Finances
Y chromosome: Sry
SRY acts on the indifferent gonad to
start the process of male sexu
Other Effects of Melatonin
How it got its name?
Rene Decartes Treatise of man (1640)- principal seat of the rational
Although such cutaneous effects of melatonin are
seen in a variety of "lower species", the hormone
does not have such effec
Steroids and its synthesis
A steroid is any of a group of natural or
belonging to the class of lipids and characterized
by a molecular core of four fused rings totaling 17
carbon atoms: three six-carbon r
Eicosanoids are specialized FA
They include prostaglandins (PG), thromboxanes
(TX), and leukotrienes (LT)
Eicosanoids have strong hormone-like actions in the
tissues where they are produced
Eicosanoids are not stored and are ve
Introduction to hormones
Hormones coordinate the physiology and
behavior of an animal by regulating, integrating,
and controlling its bodily functions.
Only cells with receptors for that hormone can be influenced
Called target cells
Interaction of a h
Steroid hormone action
(Retinoid and Thyroid have several functional
Steroid hormones are lipid soluble.
Steroids can diffuse through the membrane
They can cause:
Direct Gene Activation
Binding of ligand
Binding of DNA
Binding of co regulator
Sexual Differentiation of Brain & Physiology:
Known: The pituitary and ovary were important for ovulation.
Question: Are there differences between males and females in ability
to support ovulation?
Fasta and Blast
Heuristic algorithm for database
Why search databases?
find out if a new DNA sequence already
is deposited in the databanks.
To find proteins homologous to a putative
To find similar non-coding DNA stretches in
Alignment scoring statistics and
Analysis of Biological Sequences
Which is the better alignment?
How can we tell?
We need a scoring function. For
example, match = 2, mismatch
= -1, gap = -2. Then aln #1
scores 0 and aln #2 s
Microarray: An Introduction
Gene: a region of the human genome
coding for a protein
Biologists interested in gene function and
Studying multiple genes is time consuming
Genes are differentially expressed in.
~The origin of similarity is common
What is phylogenetic analysis and why
should we perform it?
Phylogenetic analysis has two major components:
Phylogeny inference or tree building
the inference of the br
Phylogenetic trees illustrate the evolutionary
relationships among groups of organisms, or
among a family of related nucleic acid or
E.g., how might have this family been derived
Phylogenetic trees illustrate the
evolutionary relationships among groups
of organisms, or among a family of
related nucleic acid or protein sequences
E.g., how might have this family been
derived during evolution
HIDDEN MARKOV MODELS
chain, named forAndrey Markov, is a
mathematical system that transits from one state
to another (out of a finite or countable number of
possible states) in a chain-like manner.
It is a random processendowed with
PCR & PCR Primer design
The Polymerase Chain Reaction
PCR allows one to amplify a specific DNA sequence
millions of times in just a few hours
Employs the basic biochemistry of DNA replication
particularly the concept of the primer extension
modeling and Threading
A Knowledge based protein modelling
Evolution of protein structure families
Common core = all residues that can be superposed in 3D
For proteins > 60% identical residues, the core contains > 90 % of all
Bioinformatics Scope & Applications
The application of computer technology to
the management of biological information.
Specifically, it is the science of
developing computer databases
to facilitate and expedite biologi
Central dogma of biology
DNA (Deoxyribo Nucleic Acid)
~Store genetic information, Called the blue
print of life
Hereditary information of an organism is
encoded in its DNA and enclosed in a
cell (unless it is a virus). All the
information contained in the DNA of a
single organism is its genome.
DNA molecule can be
DNA and Genome sequencing
Hereditary information of an organism is
encoded in its DNA and enclosed in a cell
(unless it is a virus). All the information
contained in the DNA of a single organism
is its genome.
DNA molecule can be thought of as a
Topics to be covered
What is sequence analysis?
Why we need it?
How we do it?
What are the tools available?
GenBank at the National Center of Biotechnology
Information, National Library of Medicine, Washington, DC
Assessing the significance of
Post alignment (of a pair
sequences) one gets a score.
How does one know whether this
score is high enough to provide
evidence of homology?
Statistical significance of sequence alignments
~ What one n
Determination of bio-molecular
Why NMR spectroscopy is good for you especially in the biological sciences
biomolecular data at atomic resolution directly
from recording a spectrum
mapping binding sites in