JAWAHARLAL NEHRU TECHNOLOGICAL UNIVERSITY HYDERABAD

Course Objectives

Knowledge on concepts of bioinformatics and biological motivations of sequence

analysis

Course Outcomes:

• 1. Understand the Central Dogma & XML (Bio XML) for Bioinformatics
• 2. Analyze Perl (Bioperl) for Bioinformatics
• 3. Illustrate Databases technology, architecture and its interfaces
• 4. Understand Sequence Alignment Algorithms, Phylogenetic Analysis

UNIT - I

The Central Dogma & XML (Bio XML) for Bioinformatics: Watson’s definition, information flow, from data to knowledge, Convergence, the organization of DNA, the organization of Proteins, Introduction, Differences between HTML and XML, fundamentals of XML, fundamentals of XML namespaces. Introduction to DTDs, Document type Declarations, Declaring elements, declaring attributes, working with entities XML Schemas, Essential Concepts, working with simple types, working with complex types, Basic namespaces issues.

UNIT - II

Perl (Bioperl) for Bioinformatics: Representing sequence data, program to store a DNA sequence, concatenating DNA fragments, Transcription, Calculating the reverse complement in Perl, Proteins, files, reading proteins in files, Arrays, Flow control, finding motifs, counting Nucleotides, exploding strings into arrays, operating on strings, writing to files, subroutines and bugs.

UNIT - III

Databases: Flat file, Relational, object-oriented databases, object Relational and Hypertext, Data life cycle, Database Technology, Database Architecture, Database Management Systems and Interfaces.

UNIT - IV

Sequence Alignment Algorithms: Biological motivations of sequence analysis, the models for sequence analysis and their biological motivation, global alignment, local alignment, End free-space alignment and gap penalty, Sequence Analysis tools and techniques.

UNIT - V

Phylogenetic Analysis: Introduction, methods of Phylogenetic analysis, distance methods, the neighbor- Joining (NJ) method, The Fitch/ Margoliash method, character-based methods, Other methods, Tree evaluation and problems in phylogenetic analysis, Clustering, Protein structure visualization and Protein structure prediction.

TEXT BOOKS:

• 1. S.C. Rastogi, N. Mendiratta, “Bioinformatics Methods and Applications”, CBS publications, 2004
• 2. James D. Tisdall, “Beginning Perl for Bioinformatics” O’Reilly media, 1st Edition, 2001

REFERENCE BOOKS:

• 1. D.R. Westhead, J.H. Parish, “Bioinformatics” Viva books private limited, New Delhi (2003)
• 2. Att Wood, “Bioinformatics” Pearson Education, 2004
• 3. Bryan Bergeron, M.D, “Bioinformatics Computing” Pearson Education, 2003