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Biology of Cells: Prokaryotic and Eukaryotic cells - E. coli and Yeast; Cell organelles and
their functions, Differences and similarities in plant and animal cells, Principles of Membrane
organization, Membrane proteins, Cell transport, Cell division - mitosis, meiosis- cell cycle;
Enzymes- classification, structure, Mechanism of action.
Cell Energetics and respiration: Energy - life's driving force; energy capture –
photosynthesis; role of ATP in energy cycle -Glycolysis, TCA cycle, Oxidative
phosphorylation; Fats and protein as alternate energy sources, Key Biomolecules - lipids,
polysaccharides, proteins, nucleic acids.
Chromosome structure in Prokaryotes and Eukaryotes, Structures of DNA - Watson and
Crick model, Different conformations, Replication; RNA secondary structure; Central dogma
of molecular biology-Transcription, Post – transcriptional modifications, codon and anticodon
concepts, Translation and Post–translational modifications; Mutation-Types, Molecular
mechanism- DNA repair mechanism- Gene regulation- operon concept - lac, trp.
Basics of recombinant DNA technology - Introduction to cloning, gene selection, restriction
enzymes-a brief account; cloning vectors – plasmid, phage vectors, cosmids, shuttle
vectors; DNA transformation; methods of clone selection and screening. Hybridization
Techniques-Southern-Northern-Western blots analysis and their applications.
Code 07PBI 1401
DNA sequencing- Maxam-Gilbert, Sanger methods, automated DNA sequencing. PCR, RFLP
and RAPD techniques, bio-chips and DNA finger printing, Applications of recombinant DNA
technology - commercial aspects of recombinant proteins.
Text Books :
Freifelder D. Molecular Biology, Jones and Bartlett Publishers Inc. 1987.
Lehninger A.L., Principles of Biochemistry, CBS Publishers and Distributors, New Delhi,
Berg, J. M. , J.L. Tymoczko and L. Stryer, Biochemistry, 5th Edition W.H. Freeman, 2002.
Reference Books :
Benjamin Lewin, Genes VIII, Pearson - Prentice Hall International Edition, New Delhi. 2004.
Watson, J.D., et al., Recombinant DNA, 2nd ed. Scientific American Books, New York, 1992.
Winnacker E. L. From Genes to Clones, VCH Weinhem, Germany, 1987.
Prokop, Ales, Bajpai, Rakesh K., and Ho, Chester S., Recombinant DNA Technology and
Applications, McGraw-Hill, New York, 1991.
CORE COURSE II
COMPUTER PROGRAMMING - I
Computer Introduction : Overview and functions of a computer System. Input and output
devices. Storage devices: Hard Disk, Diskette, Magnetic Tape, CD-ROM, DVD, Main Board :
Chips, Ports, Expansion Slots. Memory: Register, buffer, RAM / ROM, Concepts of flowchart,
‘C’ programming: Data types, operators and expressions, Hierarchy of operators
Declaring Variable and constants, Control statements including decision (if, if-else), loops
(while, do-while, for), branching (switch, break, continue), Iterative statements, Functions –
Simple, recursive functions, library functions – arguments.
Arrays, Pointers, array of pointers, Structures , unions, storage classes dynamic memory
allocation, macros and preprocessor directives, command line arguments, file Operations in
C – read, write, append operations.
Perl – Introduction, Basic Concepts, data types, variables, scalar values, Operators :
Binding, bitwise, relational , conditional, additive, multiplicative, shift and range operators,
simple and compound statements, loop statements.
Regular Expressions : Concepts, Uses , Patterns, Matching, Character classes, quantifiers,
Subroutines: semantics, passing references, prototypes
Declarations – Global, scoped declarations, Pragmas
Code 07PBI 1402
Gary Bronson J., A First book of ANSI C, 3rd edition, Thomson Asia pvt. Ltd., Bangalore,
Gottfried, B. S., Programming With C, Tata Mc Graw Hill
Lorry Wall, Tom Cheristiansan, Joe Orwant. Programming Perl, Shroff Publishers, Mumbai,
Tisdall, J., Beginning Perl for bioinformatics, Shroff publishing, Mumbai, 2006
CORE COURSE III
C Programming – Lab Exercises :
1. C Basic Input / Output Functions
2. Arrays Concepts
3. Example for Structure
4. Sample program for Pointers
5. Illustration of Conditional Statements
6. Explaining Looping Statements
7. Functions – recursive, library functions
8. Dynamic memory Allocation
9. Data Structure operations like stacks and queues
10. File Operations including read, write and appending records
Perl Programming – Lab Exercises :
1. Program to convert DNA to RNA.
2. Program to convert DNA to RNA using subroutines.
3. Program to calculate reverse complement of DNA sequence.
4. Program to read Protein Sequence Data from a file.
5. Program to. Extract Annotation and sequence from Genbank file.
6. Program to Determining Frequency of Nucleotides.
7. Program to Reading and Translating a FASTA file.
8. Program to Searching for Motif.
9. Program to Translation of DNA to Protein.
10. Program to Translation of DNA sequence in all six reading frames.
Code 07PBI 1403P
CORE COURSE – IV
BIOSTATISTICAL AND MATHEMATICAL TECHNIQUES
BIOSTATISTICS – Introduction – Applications, Collection of Data: Sampling techniques,
Graphical and diagrammatic representation.
CENTRAL TENDENCY – Arithmetic Mean, Geometric Mean, Harmonic Mean, Median, Mode
DISPERSION – Importance, range, Mean Deviation, Variance, Standard Deviation
CORRELATION – types & measures, Karl Pearson, Scatter Diagram, Rank Correlation,
Correlation for bivariate frequency distribution, REGRESSION - types, measures, Testing of
hypothesis, ANOVA – One way, Two way, STUDENT ‘t’ tests for mean and difference of
mean, CHI SQUARE distribution: independent of attributes, goodness of fit.
PROBABILITY – Basic Laws: Events, Sample Space, Addition Rule, multiplication Rule,
Random Variable, Probability Distribution, NORMAL Distribution, BINOMIAL Distribution,
Poisson distribution, Introduction to Hidden Markov model
CALCULUS – Basics, Differentiation of algebraic functions, Trigonometric functions,
Integrations – simple problems, properties of definite integrals , Uses of table of Integrals,
Numerical differentiations – Euler’s method, R-K second order method, Numerical
integration: Trapezoidal and Simpson 1/3 rule.
MATRIX – Types, Inverse, Algebra, Simultaneous Equations, Determinant, Eigen Values ,
Rank of a matrix. VECTORS – Operations, Scalar, Vector Product, Vector Calculus, Scalar
Triple Product, Divergence, Curl of Vector
Code 07PBI 1404
Reference Books :
Veer Bala Restogi, Fundamental of Biostatistics, Ane Books, New Delhi, 2006
Jorden D. W. , Smith P., Mathematical Techniques, 3 rd Edition, Oxford University Press,
New Delhi, 2004
Pillai RSM, Bagavathi,V., Chand .S “Statistics”
Ronald N.Forthofer Einsun, “Introduction to Biostatistics” Elsevier, 2006
CORE COURSE V
Analysis of DNA and Protein Sequences - distributions, frequency statistics; Protein and
Nucleic Acid Sequence Databases - PIR, Swiss-prot, GenBank; pattern and motif searches -
BLOCKS, PRINTS, PFAM; Structure Databases – PDB; Structure Classification, alignment
and analysis - SCOP, CATH, FSSP.
Sequence alignment: Scoring matrices- PAM and BLOSUM; Local and Global alignment
concepts; dynamic programming Algorithms, Needleman and Wunsch, Smith-Waterman;
Pairwise and multiple sequence alignments - Progressive alignment – Different Database
searches for homologous sequences - FASTA and BLAST.
Protein Secondary structure prediction - Chou-Fasmann rules, Gamier-Osguthorpe-Robson
(GOR) methods; Predicting 3D structure – homology modeling, threading - fold recognition
and ab initio methods - Rosetta - CASP - Molecular visualization tools - RasMol, SPDBV.
Fragment assembly - Genome sequence assembly, Gene finding methods: content and
signal methods, Background of transform techniques - Fourier Transformation analysis;
pattern recognition and gene prediction - Analysis and prediction of regulatory regions -
Neural network concepts and secondary structure prediction - RNA structure prediction.
Evolutionary analysis: Analogy versus homology; evolutionary distances – Dendrogramsclustering
methods - rooted and un-rooted tree representation - Bootstrapping strategies -
phylogenetic trees - PHYLIP.
Code 07PBI 2405
Lesk, A. M. Introduction to Bioinformatics, Oxford University Press, New Delhi
Higgins, D. and W. Taylor (Eds), Bioinformatics- Sequence, structure and databanks,
Oxford University Press, New Delhi (2000).
Durbin, R., S.R- Eddy, A. Krogh and G. Mitchison, Biological Sequence
Analysis, Cambridge Univ. Press, Cambridge, UK (1998).
Baxevanis, A. and B.F. Ouellette. Bioinformatics; A practical Guide to the Analysis of
Genes and Proteins, Wiley- Interscience, Hoboken, NJ (1998).
Michael, S. Waterman, Introduction to computational Biology, Chapman &
Gibas, C. and P. Jambeck, Developing Bioinformatics Computer Skill, 1st
Edition, O'Reilly, 2001.
CORE COURSE VI
Computer Programming – II
Client / Server: Introduction, methodology and uses. Visual Basic: Introduction to visual
basic , Data Types, Strings, Variants, Constants, Data Arrays, Looping and Iterative
Statements, Functions in Visual Basic
Tools and Controls :Command Buttons, Text Boxes, Labels, Drive List Box, Directory List
Box, Combo Box, List Box, Check Button, Option Button and Timer Control. Introduction to
data connectivity, Menu Designer, Project – form operations
Data base systems : Introduction to DBMS, DB architecture and design Data Models:
Introduction, architecture, Entity, relations, E–R Model : Components, E R diagram, Network
Model, Hierarchical Model – advantages and disadvantages, Normalization, Data abstraction,
Instances and Schemas , Introduction to Distributed Data bases
Oracle : Introduction to RDBMS, ORDBMS, Normal forms, oracle database architecture,
approaches, Data definition language, Data manipulation language, data types in Oracle,
Constraints, Operations, Queries and sub queries
SQL : Structure, Operators, tables, views, indexes, aggregate functions, Insert, Update,
delete statements, introduction to PL/ SQL and simple PL/SQL programs
Code 07PBI 2406
Reference Books :
Leon, A., and M. Leon , Essentials of Database Management System , Vijay Nicole imprints,
ISRD group, Introduction to Database Management Systems, Tata Mc Graw Hill Press Ltd,
New Delhi, 2006
Visual Basic 6 Complete, BPB publications, New Delhi, 1999.
Cornell, G., Visual Basic 6 from the ground up, Tata Mc Graw Hill, 8th Edition, New Delhi,
Vaswani, V., The complete reference My SQL, Tata Mc Graw Hill, New Delhi, 2002.
CORE COURSE VII
Lab – II for CC V, VI ( Bioinformatics and Computational Biology)
1. Study of Internet resources in Bioinformatics - E.g. NCBI, ICGEB, EMBL-EBI.
2. Searches on NCBI - PubMed bibliographic databases. Concept of boolean operators.
3. Multiple sequence alignment – CLUSTAL W
4. Phylogenetic Trees - PHYLIP
5. 5Multiple alignment - Domain / Motif databases - BLOCKS, PRINTS, - SBASE and
6. Protein Structure and Classification databases - PDB, SCOP, CATH, FSSP, PDBSUM
7. Evaluation of protein structure by Swiss PDB viewer or by any other suitable
programs like Insight-II
8. Calculation of phi - psi angles and Ramachandran plot for a given protein structure.
9. Pairwise alignment - Global alignment using Needleman-Wunsch algorithm
10. Pairwise alignmen t- Local alignment using Smith-Waterman algorithm
11.BLAST, FASTA- algorithms to search and analyze sequence databank.
Code 07 PBO 2407P
Exercises : ( VB, SQL & Office)
1. Document Preparation, Presentation – MS Office
2. Mean, Median and Mode – Excel
3. Regression Analysis - Excel
4. Basic Input Output Inputbox, Msgbox Functions
5. Forms, MDI Forms - Operations
6. Text, Label Controls
7. Data Control – Operations
8. Conditional Statements, Looping Statements
9. Graphics Programs
10.Database – Creation, Update – SQL
CORE COURSE VIII
|Biology of Cells: Prokaryotic and Eukaryotic cells E. coli and Yeast; Cell organelles and their functions, Differences and similarities in plant and animal||A study in the Conjugation between Mutant E. coli Donor and Recipient Cells|
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