BIOINFORMATICS syllabus, JNTU (2007-2008)

UNIT I: INTRODUCTION TO BIOINFORMATICS

Scope of Bioinformatics, Elementary commands and protocols, ftp, telnet, http. Primer on information theory.

UNIT-II: INTRODUCTION TO HOMOLOGY

Introduction to Homology (with special mention to Charles Darwin, Sir Richard Owen, Willie Henning, Alfred Russel Wallace).

UNIT III: SPECIAL TOPICS IN BIOINFORMATICS

DNA mapping and sequencing, Map alignment, Large scale sequencing methods Shotgun and Sanger method.

UNIT IV : SEQUENCING ALIGNMENT AND DYNAMIC PROGRAMMING

Heuristic Alignment algorithms. Global sequence alignments-Neddleman-Wunsch Algorithm Smith-Waterman Algorithm-Local sequence alignments (Amino acid substitution Matrices (PAM, BLOSUM).

UNIT V: PRIMARY DATABASE AND THEIR USE

Introduction to Biological databases, Organization and management of databases. Searching and retrieval of information from the World Wide Web. Structure databases - PDB (Protein Data Bank), Molecular Modeling Databases (MMDB). Primary Databases NCBL,EMBL, DDBJ.

UNIT-VI: SECONDARY DATABASES

Introduction to Secondary Databases Organization and management of databases Swissprot, PIR,KEGG

UNIT-VII: BIOCHEMICAL DATA BASES

Introduction to BioChemical databases-organization and Management of databases. KEGG, EXGESCY, BRENDA, WIT.

UNIT VIII: EVOLUTIONARY TREES AND PHYLOGENY

Multiple sequence alignment and phylogenetic analysis.

TEXT BOOKS:

1. Bioinformatics Basics. Applications in Biological Science and Medicine by Hooman H. Rashidi and Lukas K.Buehler CAC Press 2000.

2. Algorithms on Strings Trees and Sequences Dan Gusfiled. Cambridge University Press 1997.

REFERENCES:

1. Bioinformatics: A Machine Learning Approach P. Baldi. S. Brunak, MIT Press 1988.

2. Bioinformatics. David Mount, 2000. CSH Publications

3. Developing Bioinformatics Skills. Cynthia Gibbas & Per Jamberk

4. Genomics and Proteomics-Functional and Computational aspects. Springer Publications. Editior-Sandor Suhai.

5. Bioinformatics- Methods and Protocols-Human Press. Stephen Misener, Stephen A. Krawetz.

6. Computational Biochemistry – C.Stan ,TSAI WILEY Publications.

7. Bioinformatics – A Practical guide to the Analysis of Genes and Proteins – ANDREAS D.BAXEVANIS, B.F. FRANCIS OUELLETTE.

8. Bioinformatics – Principles and Applications – Harshawardhan P.Bal TATA MEGRAW HILL.

9. BLAST : An Essential guide Ian Korf, O’Reilly publishers.

10. Bioinformatics Computer skills Cynthia Gibas O’Reille publishers.