INSTRUCTIONAL OBJECTIVES

1. To enable the students to understand scope of Bioinformatics

2. Understanding of popular bioinformatics database

3. Learn Fundamentals of Databases and Sequence alignment

4. Approaches to drug discovery using bioinformatics techniques

UNIT I - HISTORY, SCOPE AND IMPORTANCE (9 hours) Important contributions - aims and tasks of
Bioinformatics - applications of Bioinformatics - challenges and opportunities - internet basics- HTML -
introduction to NCBI data model- Various file formats for biological sequences

UNIT II - DATABASES - TOOLS AND THEIR USES (9 hours) Importance of databases - Biological databases-
primary sequence databases- Composite sequence databases- Secondary databases- nucleic acid
sequence databases - Protein sequence data bases - structure databases - bibliographic databases -
specialized genomic resources- analysis packages

UNIT III - SEQUENCE ALIGNMENT METHODS (10 hours) Sequence analysis of biological data-Significance
of sequence alignment- pairwise sequence alignment methods- Use of scoring matrices and gap
penalties in sequence alignments- multiple sequence alignment methods - Tools and application of
multiple sequence alignment.

UNIT IV - PREDICTIVE METHODS USING DNA AND PROTEIN SEQUENCES (9 hours) Gene predictions
strategies - protein prediction strategies - molecular visualization tools-phylogenetic analysis: Concept of
trees- phylogenetic trees and multiple alignments. 72 BI - Engg. & Tech-SRM-2013

UNIT V - DRUG DISCOVERY PROCESS (8 hours) Discovering a drug - target identification and validation -
identifying the lead compound - optimization of lead compound - chemical libraries.

TEXT BOOKS

1. S.C. Rastogi & others, “Bioinformatics- Concepts, Skills, and Applications”, CBS Publishing, 2003.

2. Andreas D Baxevanis & B F Francis, "Bioinformatics- A practical guide to analysis of Genes &
Proteins", John Wiley, 2000.

3. T K Attwood, D J parry-Smith,” Introduction to Bioinformatics”, Pearson Education, 1st Edition, 11th

Reprint 2005.

REFERENCES

1. C S V Murthy,” Bioinformatics”, Himalaya Publishing House, 1st Edition 2003

2. David W.Mount “Bioinformatics sequence and genome analysis”, Cold spring harbor laboratory press,
2004.

3. S. Ignacimuthu, S.J., “Basic Bioinformatics’, Narosa Publishing House, 1995.

BI1001 COMPUTATIONAL BIOLOGY

INSTRUCTIONAL OBJECTIVES

1. Introduce the concept of Algorithms and their applications in Biology.

2. Overview of different types of algorithms

3 Description and applications of Greedy algorithms, Dynamic Programming

4 Description and applications of Graph algorithms, Clustering algorithms.

UNIT I - INTRODUCTION (10 hours) Algorithms and Complexity- Biological algorithms versus computer
algorithms - The ‘Change problem’ - Recursive Algorithms - Iterative versus Recursive Algorithms - Big-O
Notations – Algorithm design techniques and the different types of algorithms.

UNIT II - GREEDY ALGORITHMS (10 hours) Molecular Biology Primer - Exhaustive Search: Mapping
Algorithms – Motif Finding problem - Search Trees - Finding a Median String. Greedy Algorithms:
Genome Rearrangements - Sorting by Reversals - Approximation Algorithms - A Greedy Approach to
Motif Finding.

UNIT III - DYNAMIC PROGRAMMING ALGORITHMS (8 hours) DNA Sequence comparison - Manhattan
Tourist Problem - Edit Distance and Alignments - Longest Commons Subsequences - Global Sequence
Alignment - Scoring Alignment - Local Sequence Alignment - Alignment with Gap Penalties - Multiple
Alignment.

UNIT IV - GRAPH ALGORITHMS (8 hours) Graphs - Graphs and Genetics - DNA Sequencing - Shortest
Superstring Problem - DNA arrays as an alternative sequencing techniques - Sequencing by Hybridization
- Path Problems - Fragment assembly in DNA Sequencing - Protein Sequencing and Identification - The
Peptide Sequencing Problem – Spectrum Graphs. 74 BI - Engg. & Tech-SRM-2013

UNIT V - CLUSTERING AND TREES (9 hours) Gene expression analysis - Hierarchical clustering-k-means
clustering - Clustering and corrupted Cliques - Evolutionary Trees - Distance-based tree reconstruction -
Reconstruction trees from additive matrices - Evolutionary trees and hierarchical clustering - Character-
based tree reconstruction - Small and large Parsimony Problem - Hidden Markov Models.

TEXT BOOKS

1. Neil C. Jones and Pavel A. Pevzner, “An Introduction to Bioinformatics Algorithms”, MIT Press, First
Indian Reprint 2005

REFERENCES
1. Gary Benson Roderic, “Algorithms in Bioinformatics”, Springer International Edition, First Indian
Reprint, 2004.

2. Gusfields G, “Algorithms on strings, trees and sequences- Computer Science and Computational
Biology”, Cambridge University Press, 1997.

3. Steffen Schulze-Kremer, “Molecular Bioinformatics: Algorithms and Applications”, Walter de Gruyter,

1996.