RGTU/RGPV MCA Bioinformatics Syllabus MCA-505 Elective- EIII (c ) 5th -Fifth sem Bioinformatics Syllabus

RGTU/RGPV MCA-505 Elective- EIII (c ) Bioinformatics Syllabus
MCA 5th Sem Bioinformatics Syllabus
MCA 5th - Fourth Semester Syllabus

MCA-505 Elective- EIII (c ) Bioinformatics Course Contents:

UNIT-I
Fundamentals of Bioinformatics and Information Technology :
Introduction to bioinformatics, experimental sources of biological data fundamentals of molecular biology available databases operating system, inclusing windows and Unix networks-including the intranets and the Internet.
Analytical science and Bioinformatics : High throughput sequencing, experimental determination of protein structures, Gene expression monitoring, proteomics, metabiomics.

UNIT-II
Protein Information resources :
Introduction, biological databases, primary sequence databases, composite protein sequence database, secondary databases, composite protein pattern databases, structure classification databases, web addresses.
Genome information resources : Introduction, DNA sequence databases, specialised genomic resources.
DNA Sequence analysis : Introduction, why analyse DNA, Gene structure and DNA sequences, features of DNA sequence analysis, issues in the interpretation of EST searches, two approaches to gene hunting, the expression profile of a cell, cDNA libraries and ESTs, different approaches to EST analysis, effects of EST data on DNA databases.

UNIT-III
Pairwise alignment techniques :
Introduction, database searching, alphabets and complexity, algorithms and programs, comparing two sequences a simple case, sub-sequences, identity and similarity, the dotplot, local and global similarity, global alignment the needleman and wunsch algorithm, local alignment the smith waterman algorithm, dynamic programming, pairwise database searching.
Multiple sequence alignment : Introduction, the goal of multiple sequence alignment, multiple sequence alignment a definition, the consensus, computational complexity, manual methods, simultaneous methods, progressive methods, database of multiple alignment, searching databases with multiple alignments.
Secondary database searching : Introduction, why bother with secondary database searches, what is a secondary database.

UNIT-IV
Bioinformatics tools :
Visualisation of sequence data, sequence alignment, homology searching, inclusing BLAST, gene expression informatics, introduction to gene finding.
Building a sequence search protocol : Introduction, a practical approach, when to believe a result, structural and functional interpretation.
Analysis packages : Introduction, what’s in an analysis package, commerical databases, commerical software, comprehensive packages, packages specialising in DNA analysis, intranet packages, internet packages.

UNIT-V
Applications and commercial aspects of Bioinformatics : Drug discovery, genetic basis of disease, personalised medicine and gene-based diagnostics, legal, ethical and commercial ramifications of bioinformatics.
Perl Programming : Data manipulation, file maintenance, pipelining, packaging and interfacing system facilities.
Macromolecular Modelling and Chemoinformatics : Acquisition of chemical information, including molecular structure from databases visualisation of molecules simulation of molecular interaction introduction to industry standard modelling software.

BOOKS
1. Attwood TK & Parry-smith DJ “Introduction to Bioinformatics” 2001, Pearson Education Asia.
2. Setup Joao & Meidanis Joa “Introduction to computational Molecular Biology” PWS Publishing Company, 1997 (An international Thouson publishing company).
8. Andreas D. Baxevan’s & B.F. Francis Quellette, “Bio Informatics: A Practical guide to the analysisof Genes & Proteins”, Second edition 2001, A John wiley & Sons.
9. Martin Tompa Lechre notes on Biological sequence Analysis, Department of Computer Science & Engineering, university of wasnington, seattle USA http:/www.cs.washington.edu/education/ courses / 527/ oowi/
10. Jean Michael “Bioinformatics : A beginner’s Guide”, Wiley India.
Note : Paper is to be set unit wise with internal choice.

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