BBL 434 – Bioinformatics

D. Sundar

Lecture 01
Schedule of lectures and
laboratory hours
3 credits (2-0-2)

Lecture hours – Thursday & Friday (11 AM)

(Buffer lecture hour – Tuesday (11 AM)

Laboratory – Thursday/Friday (3 - 5 PM)

(in CSC – PCLab 3)

(Lab classes will start from Jan 9 onwards)

 Grading
•  THEORY (80 points)
–  2 Minor tests (20 + 20 points)
–  1 Major test (30 points)
–  Quiz (surprise) (10 points)

•  LABORATORY (20 points)

–  Lab Assignments (10 points)
–  Major Test (10 points)

TOTAL 100

* No request for a re-test will be entertained

 Attendance

•  Attendance should be marked through Timble only.

•  No paper attendance will be maintained.

•  If a student’s attendance is less than 75%, the

student will be awarded one grade less than the
actual grade that he(she) has earned
 Assignment, Lab Record
and Late Policy
•  Throughout the semester, there will be a number of
laboratory exercises that will be made available
every week.

•  You are required to work on the exercises then &

there…….and submit the recordings/solutions by
the beginning of a new week. Your submission of
lab exercise solutions is due for continuous
evaluation at the beginning of the each week.

•  Late lab records submission will not be accepted

for evaluation.
 Changes to be noted

•  In the next 3 weeks, there will be a slight change in

routine (days of lecture classes)

•  Not possible to follow the Thursday/Friday schedule

for lectures (becos of some Institute level
assignment). Tuesday slot will also be used.

•  Lectures up to Minor-1 will be held on

Jan 02, Jan 07, Jan 16, Jan 17, Jan 21, Jan 23, Jan 24, Jan 30, Jan 31
What is Bioinformatics?
 My understanding
NIH definitions

•  Bioinformatics: Research, development, or application of

computational tools and approaches for expanding the use
of biological, medical, behavioral or health data, including
those to acquire, store, organize, archive, analyze, or
visualize such data.

•  Computational Biology: The development and

application of data-analytical and theoretical methods,
mathematical modeling and computational simulation
techniques to the study of biological, behavioral, and social
systems.
 Tentative schedule of topics

•  An overview
•  Applications
•  Molecular biology for bioinformatics
•  Biological data acquisition
•  Biological databases – Format and annotation
•  Biological data – access, retrieval & submission
•  Sequence similarity searches
 Tentative schedule of topics

•  Pairwise sequence alignment

•  Multiple sequence alignment
•  Gene prediction
•  Phylogenetic analysis
•  Understanding sequence-function relationships
•  Genome analysis
•  Molecular modeling in drug design
 Reference Books
•  Bioinformatics: Sequence and Genome Analysis
Author - DW Mount
Press - Cold Spring [CBS Publishers, India edition].

•  Bioinformatics: a practical guide to analysis of genes & proteins

Authors - AD Baxevanis & BFF Ouellette
Press - Wiley Interscience

•  Bioinformatics and Functional Genomics

Author - Jonathan Pevsner
Press - John Wiley & Sons

•  Bioinformatics-related Journals
Bioinformatics, BMC Bioinformatics, BMC Genomics, Nucleic Acids Research,
Genome Research, Genome Biology, Computational Biology, Protein Science,
Protein Structure Function and Bioinformatics, etc
 Bioinformatics
•  collection and storage of biological information
(originally)
•  development of algorithms and statistical models to
analyze biological data

•  Structural Biology Computer Science

•  Biochemistry Statistics
•  Physical chemistry Mathematics
•  Molecular biology
•  Genomics, Bioinformatics
 What we need bioinformatics ?!

Flakes of Knowledge

Piles of Information

Co l i
E.

Large amounts of data available

Source – J. Bacteriology 188(10): 3431-3432, 2006

 Why is bioinformatics needed?

•  Genome sequencing, high throughput gene

expression analysis, etc lead to large amounts of
data to be analyzed

•  Leads to important discoveries

•  We can generate knowledge and save time/

money in validation
 Overview of Molecular Biology
•  Cells
•  Chromosomes
•  DNA
•  RNA
•  Amino Acids
•  Proteins
•  Genome/Transcriptome/Proteome
 Central Dogma

DNA
↓
RNA
↓
PROTEIN
Central!Dogma!
 What is a Gene?
•  the physical and functional unit of heredity
that carries information from one
generation to the next

•  DNA sequence necessary for the

synthesis of a functional protein or RNA
molecule
 Genome
•  chromosomal DNA of an organism

•  number of chromosomes and genome size

varies quite significantly from one organism to
another

•  Genome size and number of genes does not

necessarily determine organism complexity
Comparative genome sizes of humans
and other model organisms
Organism Estimated size Chromosome Estimated
(base pairs) number number of
genes
Human 3 billion 46 ~ 25,000
Mouse 2.9 billion 40 ~ 25,000
Fruit fly 165 million 8 13,000
Plant (Arabidopsis) 157 million 10 25,000
Roundworm 97 million 12 19,000
Yeast 12 million 32 6,000
Bacteria (E. coli) 4.6 million 1 3,200

NCBI Genome
 Transcriptome
•  complete collection of all possible mRNAs
(including splice variants) of an organism.

•  regions of an organism s genome that get

transcribed into messenger RNA.

•  transcriptome can be extended to include all

transcribed elements, including non-coding
RNAs used for structural and regulatory
purposes.
 Proteome
•  the complete collection of proteins that can
be produced by an organism.