Advanced Diploma Course in Bioinformatics

 

School of Biotechnology

Madurai Kamaraj University

 (Effective from the Academic year 2005-2006)

 

Preamble

 

The effective use of bioinformatics tools is expected to create significant job opportunities.  The syllabus of the Advanced Diploma Course in Bioinformatics was revised and this revised course content could lead to better understanding of the subject and should make the students better equipped for the job market in Academic as well as industrial sectors.

 

1.             Eligibility for admission:

 

M.Sc., degree (50% minimum) in Physical or Mathematical or Life Science (Physics, Chemistry, Mathematics, Biotechnology, Biophysics, Botany, Zoology, Biochemistry, Microbiology, Pharmacology, Agriculture or equivalent) or Computer Sciences or    M.Tech, or M.B.B.S degree of a recognized Indian or Foreign University. 

 

2.          Maximum number of candidates:

 

          1.  Open competition                     – 10   and 

2.  Industry sponsored candidates              5.

 

 3.             Processing of application:

 

Applicants will be selected on an all India basis.  All eligible applicants will be called to write an entrance examination.  Candidates are screened based on their ranking at the entrance examination and will be called for a personal interview.  GATE or NET qualified candidates will be given additional advantage.  Final selection will be based on Entrance examination (80%) and personal interview (20%).  All candidates including sponsored candidates should undergo the above selection procedure. 

 

 

4.             Counseling:

 

          Each course instructor will be the overall counselor for that course.

 

 

5.             Course structure:

 

The course is organized on semester basis with a total of two semesters.

 

6.             Evaluation - (General):

 

i.                   Marks system follows the University regulations. 

 

ii.                 For each course, 40% of the total marks is allotted to internal assessment, 60% for University examination.    The course instructor will carry out the internal assessment for each paper.   This will consist of at least two mid term tests (or assignments). A Comprehensive external examination at the end of the semester will be as per University regulations.

 

iii.               The conduct of supplementary examination will follow the University regulation for postgraduate diploma courses.

 

iv.               Project evaluation: The project dissertation carries a total of 400 marks.   The viva-voce examination is part of dissertation, which carries 100 marks.  

 

7.       Transitory Provision:

 

A transitory provision of two years has been given for the benefit of the students who come under the old syllabus (effective from the year 2001-2002), i.e., they need to clear all the papers including the practical and project work by May 2007, in order to qualify for the Diploma.

 

 

 

8.Tabulation on final results:

 

The marks obtained in each course, internal and external will be entered separately.

 

For a pass, the student should have a minimum of 50% marks in the final examination and a minimum of 50% in the total  (internal and final) marks for each course. Of the total marks of 1400 covering both semesters 60% and above will be declared I class, 50-59% will be declared II class.

 

 


 

Advanced Diploma Course in Bioinformatics

 
Scheme of Examination

 (Effective from Academic Year 2005-2006)

 

I Semester

                                                                                       MARKS

 

                                                                                                                  Internal       Final     Total

 

Paper-I               ADC101 Fundamentals of                                                 40        60            100

                                        Bioinformatics

                                               

Paper-II              ADC102 Structural Biology                                      40        60        100     

 

Paper-III             ADC103 Molecular Biology of the Gene                        40          60        100

 

Paper-IV             ADC104 Molecular Graphics and Drug Design            40        60        100

 

Paper-V                 ADC105 Programming for Bioinformatics                40       60        100

 

Practical-I              ADC106 Lab in Sequence Analysis                                      40         60                100

                         

Practical-II             ADC107 Lab in Computer Applications                           40       60        100

                         

 

II Semester

 

Paper VI            ADC201 Genomics, Functional Genomics                     40            60            100

                                        and Proteomics

 

Practical III            ADC202 Applications of Molecular Graphics            40            60            100

 

Practical IV            ADC203 Lab in Database and Web Programming            40            60            100

 

Project             ADC204                                                                                            400

                                                                                                                                    -------                                                               Total                                                                        1400

                                                                                                                                    -------

 

 

 

 

 

 

Advanced Diploma Course in Bioinformatics

CURRICULUM

(Effective from Academic Year 2005-2006)

 

Semester I

 

ADC 101. Fundamentals of Bioinformatics

 

1.     Overview:

Biological Literature Information access, storage and retrieval; Genomics; Proteomics; Structural Genomics; Pharmainformatics; Pharmacogenomics: Population genomics; Biodiversity; Systems Biology; Hardware and Software approaches

2.     Collecting and Storing Sequence Data:

Genomic Sequencing; Sequence assembly; Submission of Sequences; Sequence accuracy; Sequence databases; Sequence formats; Conversion between formats; Database browsers; EST databases; SNP databases; Annotation and Archival

3.     Sequence alignment and applications:

Uses; Choice to be made for alignment; Scoring Matrices; Homology and related concepts; Dot matrix methods; Dynamic Programming methods for global and local alignments; Database searching – FASTA, BLAST; Statistical and biological significance

4.     Nucleic acid sequence analysis:

Reading frames; Codon Usage analysis; Translational and transcriptional signals; Splice site identification; Gene prediction methods; RNA fold analysis

5.     Multiple Sequence alignment and applications:

Uses; Methods available- Iterative alignment, Progressive alignment – ClustalW, T-Coffee; Profile Methods – Gribskov profile, PSI-BLAST, HMM ; Clustering and Phylogeny; Methods for Phylogeny analysis: Distance and Character based methods; Motif detection ; Protein family databases; Use of Structure based sequence alignment

 

 

6.     Protein sequence analysis:

Compositional analysis ; Hydrophobicity profiles; Amphiphilicity detection; Moment analysis; Transmembrane prediction methods; Secondary structure prediction methods

 

References:

 

1.     Current Protocols in Bioinformatics, Edited by A.D. Baxevanis et al, Wiley Publishers 2005

2.     Bioinformatics by David W. Mount, Cold Spring Harbor Laboratory Press, 2001, ISBN 0-87969-608-7

3.     Computational Molecular Biology  by P. A. Pevzner, Prentice Hall of India Ltd, 2004 ISBN 81-203-2550-8

4.     Fundamental concepts of Bioinformatics by D.E. Krane and M.L Raymer, Pearson Education 2003  ISBN 81-297-0044-1

 


 

ADC 102. Structural Biology

 

1.     Basic structural principles, building blocks of proteins, motifs of protein structures, alpha domain structures, alpha/beta structures, beta structures.

2.     DNA structures, DNA recognition in prokaryotes, DNA recognition in eukaryotes, specific transcription factors, enzyme catalysis and structure.

3.     Membrane proteins, signal transduction, proteins of the immune system.

4.     Folding and flexibility, Prediction, engineering and design of protein structures, Structure of spherical viruses.

5.     Determination of protein structures by X-ray and NMR methods.

 

References:

 

1.Protein Structure, stability and folding Ed. K.P. Murphy (2001) Humana Press.

2. Introduction to protein architecture Arthur M. Lesk (2001) Oxford University Press.

3. Introduction of Macromolecular Crystallography – A. Mcpherson (2003) John Wiley Publications.

4.Introduction to protein structure, Branden, Carl and Tooze, John Garland Publ. Inc., 1991 302p $ 27.55

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

ADC 103. Molecular Biology of the Gene

 

1.     Organisation of the genes across the living systems: Basic architecture and the modified organization, Interrupted genes, gene families etc. Genome Organisation and content.

2.     Transcription and its regulation. Prokaryotic and Eukaryotic transcriptional machinery. Transcriptional control.

3.     Protein synthesis. Prokaryotic and eukaryotic translational apparatus, Translational regulation.

4.     Protein localization. Motifs involved in translocation. Secretion machinery

5.     Regulatory circuits, operons and higher order regulatory systems. Phage systems, Transposable elements.

 

Reference:

 

1.     Benjamin Lewin. Genes VIII Pearson , Prentice Hall. 2004.

2.     Genomes T.A. Brown, Bios. 2002.

 

 


 

ADC 104. Molecular Graphics and Drug Design

 

1.     Computational Chemistry: Concepts of computational chemistry, Born-Oppenheimer approximations, Application of Hartree-Fock equations to molecular systems, approximate Molecular orbital theories, semi-emperical methods

2.     Molecular mechanics: general features, bond stretching, angle bending, improper torsions, out of plane bending, cross terms, non-bonded interactions, point charges, calculation of atomic charges, polarization, van der Waals interactions, hydrogen bond interactions, Water models, Force fields, all atoms force field and united atom force field

3.     Energy minimization: statement of the problem, Derivatives; Non-derivative minimization methods: The simplex method, Sequential univariative method. Derivative methods: First-order Derivative, Steepest decent methods, Conjugate gradients.  Second-order Derivative: Newton-Raphson method, Minima, Maxima, saddle points, convergence criteria

4.     Simulation methods:  Time averages, ensemble averages, Molecular dynamics methods, Monte Carlo methods, Differences between MD and MC, Energy, Pressure, Temperature, Temperature dynamics: Simulated Annealing procedure. Initial configuration,  Periodic Boundry conditions, Solvent access, Equilibration, cutoffs, Problems and overcoming it, Time step, Constraint dynamics, Systematic methods, Random search methods, Distance geometry, Use of distance constraints in NMR

5.     Docking and Drug Design: Discovery and design of new drugs, computer representation of molecules, 3D database searching, Deriving and using the 3D Pharmacophore , constrained systematic search, Clique detection techniques, Maximum likelihood method, molecular docking: scoring functions, Pharmacophore keys, Structure-based De Novo Ligand design, Quantitative Structure Activity Relationship QSAR, Combinatorial libraries, design of ‘Drug like’ libraries 

 

 

References:

 

1.Molecular Modelling Principles and Applications, Andrew R.

   Leach, II ed. 2001. Prentice Hall

2.Current Protocols in Bioinformatics, Wiley Publishers, 2005

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

ADC 105. Programming for Bioinformatics

 

1.     Programming in C

Introduction, Data types, Operators, Expressions, Control Flow,  Structures, Input and Output, Functions, Pointers and References, String Processing, File Handling

2.     Perl Programming

Introduction, Basic Operators and Control Structures, Scalars, Lists, Hashes, File Manipulation, Pattern Matching and Regular Expressions, Subroutines, Text and String Processing, Mathematical Functions, Special Variables, References, Aggregate data structures, Using Modules

3.     Python Programming

Overview, Datastructures, Control Flow, Modules, Basic I/O, Exception       Handling, Regular Expressions, File Manipulation, Classes, Standard library

4.     Database Management systems

Overview of DBMS, Relational database management fundamentals, Structured Query Language (SQL), SQL syntax and Specifications, Simple queries using MySQL

5.     Web Technologies

History of Internet, Internet Terminologies,  Basic Web concepts, Client, Server model, Retrieving data from Internet,  Protocols, HTML Specification and  Syntax, XML Basics, Document Type Definitions, Style Sheets, Supplemental Technologies, XML Applications, Java Script, Java, OOP paradigms, Java Environment, JVM, Simple Applet Programming, Multithreading, Applets, Components for Java GUI, Java I/O and Networking

6.     Common Gateway Interface

CGI concepts, HTML tags emulation, Server browser communication, E-mail generation, Using CGI.pm, CGI client side Applets, CGI Server side Applets, Authorization and Security, Database support in Web Applications

7.     Machine Learning Techniques

Hidden Markov Models, Theory, Viterbi Algorithm, Finding the most likely path, Baum Welch Algorithm, Stochastic Context Free Grammars, EM Algorithm, Genetic Algorithms, Neural Networks fundamentals, Decision Trees

 

 

 

References:

 

1.     The C Programming Language, B.W.Kernighan and D.M. Ritchie 2nd Edition. Prientice Hall of India.

2.     Programming Perl – Larry Wall, Tom Christiansen & John Orwant 3ed 2000- O’ Reilly

3.     Programming Python – Mark Lutz – 2nd Ed., O’ Reilly

4.     SQL in a Nutshell – K.Kline with  D.Kline O’Reilly ISBN:I:56592-744-3

5.     Machine Learning, Tom Mitchell, McGraw Hill , 1997

6.     Using HTML 4, XML and JAVA, Eric Ladd, J.O’Donnell, Prentice Hall of India QUE, 1999

7.     Java2: The Complete Reference, P.Naughton and H. Schildt, 3rd ed. Tata McGraw Hill

8.     CGI Manual of Style, Robert McDaniel, Ziff Davis Press, 1996

http://docs.rinet.ru/CGIM/

9.     XML Bible 2nd ed. Elliotte Rusty Harold IDG Books India (P) ltd.


 

ADC 106. Lab in Sequence Analysis

 

1. Introduction to sequence analysis software

Installation of EMBOSS; Use of EMBOSS and GCG; BioEdit;

Public Domain Software; Internet access to software and databases

2. Accessing  Biological Databases:

Retreiving protein and nucleic acids sequences, structures, EST sequences, SNP data and biomedical information from databases; Using database browsers and genome browsers; Converting sequences between different formats; Using sequence editors; Sequence assembly

3.  Nucleic acid sequence analysis:

Detecting ORFs; Identification of translational and transcriptional signals; Gene predictions; Codon usage; RNA Fold analysis

4. Sequence alignment and applications:

Pairwise alignment – Dot matrix comparisons, Global and Local alignment; Database searching – different pairwise methods; Use of scoring matrices and gap penalties; Statistical vs Biological significance; Handling large datasets; genome comparisons.

5. Multiple sequence alignment and applications:

Use of Mutliple sequence editors; Progressive alignment and iterative alignment approaches; Use of Profile methods;  Motif detection; Clustering and Phylogeny approaches; Protein family classification

6. Protein sequence analysis:

Composition analysis; Hydrophobicity and amphilicity analysis; Transmembrane predictions; Secondary structure prediction

7. Integrating information:

Report generation; Making presentations of results; Placing analysis in biological context; Limits of analysis

 

 


ADC 107  Lab in Computer Applications

 

 

1.    Programming in C

Simple programs implementing  basic algorithms, String processing  and  File Handling

2.     Basic Perl Programming

Regular expressions, File Handling, Text and String processing, Creating Simple Packages

3.     Basic Python Programming

Regular expressions and String Processing, Simple Bioinformatics applications using Biopython

4.     HTML and Javascript Programming

5.     Developing Simple Web Pages  Using HTML and Javascript

 

Reference:

 

1.     The C Programming Language B.W. Kjernighan and D.M.Ritchie 2nd  ed.  Prentice Hall, India

2.     Perl CookBook – T.Christainsen and N.Torkington 2nd ed. 2003 O’Reilly

3.     http://zoic.org/tranining/nothtml/perldb.pdf

4.     http://doc./bioperl.org/

5.  Text Processing in Python – D.Mertz online at http://gnosis.cx/TpiP/

Semester II

 

ADC 201. Genomics, Functional Genomics  and Proteomics

 

1. Genome organization in pro and eukaryotes; whole genome sequencing technologies; assembly of sequence reads; annotation and other methods of genome; sequence analysis; minimal genome concept.

2. Functional genomics of microbes, plants and animals; Transcriptome analysis methods, microarrays and serial analysis of gene expression. Data bases of expressed sequence tags. Data mining.

3. Proteomics of selected systems, methods and applications of proteome analysis. Expression proteomics; 2D and multidimensional chromatography. MALDI method and applications in protoemics. Protein interaction analysis.

 

References:

 

1.Genomics: The Science and Technology Behind the Human

   Genome Project (2000). Edited by C.Cantor and C.L.Smith, Wiley

   -Interscience, New York.

2. Genome Analysis – A practical Approach (1995) by J.M. Davies,

    Oxford University Press, Oxford.

          3. Genome Mapping – A Practical Approach (1997) by P.H. Dear, 

              Oxford University Press, Oxford.

     4. Genome Analysis – A Practical Approach (1990). Edited by K.E

         Davies, IRL Press, Oxford.

5.The Human Genome (1992) by T. Strachan. BIOS Scientific

    Publishers Limited, Oxford.

     6.  Reviews and Articles from Journals such as Nature, Science,

               PNAS  (USA), Nucleic Acids Research, Trends Series & Current

               Opinion Series.

7.Proteine Research: New Frontiers in Functional Genomics (1997).

   Edited by M.R. Wilkins, K.L. Williams, R.D.Appel and D.F.

   Hochstrasser, Springer – Verlag, New York.

8.Expression Genetics: Acclerated and High Throughput Methods

   (1999) Edited by M.McClelland and A. Pardee, Eaton Publishing,

   MA.

 

9. 2-D Proteome Analysis Protocols (1998). Edited by A.L. Link,

     Humana Press, Totowa, NJ.

          10. Proteins and Proteomics. 2002. R.J. Simpson. Cold Spring Harbor

                Lab. Press. New York.

 


 

ADC 202. Applications of Molecular Graphics

1.     Molecular Mechanics, The molecular potential energy function, The empirical force field,  Sources of force field data,  Some examples of important force fields

2.     Energy Minimisation: First derivative techniques: steepest descent and conjugate gradients, Second derivative techniques: Newton-Raphson,  Global optimisation

3.     Molecular Dynamics and Monte Carlo Simulations: Brief introduction to statistical mechanics: Molecular dynamics simulations,  Monte Carlo simulations

4.     Conformational Analysis: Systematic methods, Random search methods, Distance geometry, Molecular dynamics

5.     Solvation:  Brief comparison of different solvation methods, Periodic boundary conditions..

6.     Structure-Based Drug Design: Homology Modelling, Predicting protein-biomolecule structures, The search problem, Constraint-based methods, DOCK algorithm, Complete search of conformational space, Virtual screening, Conformational flexibility, Stochastic search methods, Combinatorial search methods, Template forcing

 

Referenences:

1.Sybyl 6.6, 1999, Tripos Inc., 1699 South Hanley Road, St.Louis, MO 63144-2913.

2.Insight II User Guide, October, 2000, San Diego, Accelrys Inc., 2000.

3.  Molecular Modelling, Principles and Applications, IInd Edition, A.R. Leach, 2001, Prentice Hall

 

 

 

 

 

 


 

ADC 203.  Lab in Database and Web Programming

 

 

1.     Advanced Perl Programming

Database programming using Perl,  Berkeley DB  features, Using DBM module, Using DBI for SQL queries, Perl Graphics, Using the GD.pm graphics library, Using LWP, Socket Programming, Simple Bioinformatics Applications using BioPerl

2.     Java Programming

Creating Simple Applets, Java Graphics using Image class, Using BioJava

3.     Database Management Systems

Creating databases, Creating tables,  Dropping Tables, Primary and Secondary Keys, Data Validation, Simple queries using MySQL , Cursors , Stored Procedures

4.     Common Gateway Interface

Developing CGI applications using Perl, CGI.pm , A simple shopping cart example, Counters, SSI, Managing Cookies  

5.     XML

XML Processing in Perl, SAX, Generating XML documents from Databases, XML::DBMS, XML::Generator::DBI, XML::Parser - RPC::XML

 

Reference:

1.     Programming Web Graphics with Perl and GNU Software – S.Wallace, Ist ed. 1999

2.     XML and Perl Ist ed, M.Riehl and L. Sterin Pearson Education 2002

3.     SQL in a Nutshell – K.Kline with D.Kline O’Reilly, ISBN 1-56592-744-3

 

 

 

ADC 204.   Project


 

Advanced Diploma Course in Bioinformatics

 

School of Biotechnology

 Madurai Kamaraj University

(Effective from Academic Year 2001-2002)

Examination Pattern

 

Model Question pattern for Papers

ADC101, ADC102, ADC103, ADC104, ADC105 and ADC201

 

Time:  3 hours                                                           Total Marks: 60

 
Part A

Answer any 10 questions out of 12                                             10X2 = 20

 

Part B

Answer any 4 questions out of 6                                                4X5 = 20

 

Part C

Answer any 2 questions out of 3                                              2X10 = 20

 

 

Model Question pattern for Papers

ADC106, ADC107, ADC202 and ADC203

 

Time:  3 hours                                                           Total Marks: 60

 

 

 

Part A

Answer any 1 question out of 2                                                       1X10 = 10

 

Part B

Answer any 1 question out of 2                                                         1X20 =20

 

Part C

Answer any 1 questions out of 2                                              1X30 = 30