Advanced
Diploma Course in Bioinformatics
Madurai
Kamaraj University
(Effective from the Academic year 2005-2006)
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
(Effective from Academic Year 2005-2006)
I Semester
MARKS
Internal Final Total
Paper-I ADC101 Fundamentals of 40 60 100
Bioinformatics
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)
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
Introduction, Data types,
Operators, Expressions, Control Flow,
Structures, Input and Output, Functions, Pointers and References, String
Processing, File Handling
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
Overview, Datastructures,
Control Flow, Modules, Basic I/O, Exception Handling, Regular Expressions, File Manipulation, Classes,
Standard library
Overview of DBMS, Relational
database management fundamentals, Structured Query Language (SQL), SQL syntax
and Specifications, Simple queries using MySQL
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
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
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
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
Simple
programs implementing basic algorithms,
String processing and File Handling
Regular
expressions, File Handling, Text and String processing, Creating Simple
Packages
Regular
expressions and String Processing, Simple Bioinformatics applications using
Biopython
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
5. Text
Processing in Python – D.Mertz online at http://gnosis.cx/TpiP/
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
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
Creating Simple Applets,
Java Graphics using Image class, Using BioJava
Creating
databases, Creating tables, Dropping
Tables, Primary and Secondary Keys, Data Validation, Simple queries using MySQL
, Cursors , Stored Procedures
Developing
CGI applications using Perl, CGI.pm , A simple shopping cart example, Counters,
SSI, Managing Cookies
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
School of
Biotechnology
Madurai Kamaraj University
(Effective from Academic
Year 2001-2002)
Model Question
pattern for Papers
ADC101,
ADC102, ADC103, ADC104, ADC105 and ADC201
Time: 3 hours Total Marks: 60
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
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