Bio-Informatics Syllabus-09

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                       SYLLABUS FOR SVURESET-2009

Enzymes and metabolism: Kinetic analysis of enzymes (Km and Vmax); Factors
influencing enzyme catalysis; Allosteric enzymes, Mechanism of enzyme action,
Immobilized enzymes, Isozymes; Metabolism: Mitochondrial electron transport
system, Glycolysis, TCA cycle, Beta oxidation, Transamination and deaminaiton

Cell signaling molecules: Steroid and peptide hormones, Nitric oxide, Carbon
monoxide, neurotransmitters (ACh, Catecholamines and Amino acids); Cell surface
receptors: G protein-coupled receptors, Tyrosine kinases, Cytokine receptors, Ras,
Raf and MAP kinase pathways

Humoral immunity: Immunoglobulin (Fine structure and types), The complement
system, Classical and alternate pathway and Inflammation, Mechanism of cell-
mediated immunity, Major Histocompatability complex; Active and passive
immunity, Autoimmunity, Transplantation, Antigen-Antibody interactions: Affinity,
Avidity, Cross – reactivity, Precipitation reactions, Agglutination reactions and

Unit: II
C-value paradox, Cot value; Structure of gene (Cistron, Muton, Recon and Cis-trans
test) DNAdamage and repair: Biological indication of repair, photo reactivation,
Excision repair, Recombination repair, SOS repair and Mismatch repair; Mechanisms
involved in Replication, transcription and Translation; Induction, Repression, Lac
operon and Lambda operon.
Molecular vectors: Cloning, Shuttle, Expression and Binary vectors; Restriction
endonucleases; DNA and RNA polymerases, Nucleases, Kinases, Phosphatases and
Methylases, Western, Northern and Southern blotting
Construction of cDNA and genome libraries; Polymerase Chain Reaction (PCR) and
its applications; Sequencing of nucleic acids: Maxam and Gilbert chemical
degradation and Sanger’s dideoxy chain termination methods and site-directed

Descriptive Statistics (Mean, Median and Mode); The concept of probability,
Binomial and Normal distributions, properties and applications; Statistical tests of
significance: Student's t-test, F-test and Chi-square tests and their applications;
Standard Deviation; ANOVA

Chromatography (Paper, Thin layer, Ion exchange, HPLC); Electrophoresis (Types of
electrophoresis, Paper and gel (Starch, Arcylamide and Agarose); Spectroscopy (UV-
Vis. Spectrophotometry, Infrared spectroscopy, Atomic Absorption Spectroscopy and
fluorescent spectroscopy); X-ray diffraction and X-ray crystallography, ESR and
NMR Spectrophotometry

2D gel electrophoresis, Tandem Mass Spectrometry (MS/MS), Peptide mass
fingerprinting (PMF), Post-translational modifications: POSRT, Signal P, Chloro P,
Target P and Predator; Primary and secondary structure analysis and prediction;
Protein folding (Ramachandran plot, Side chain conformation, Molecular
chaperones), Polymorphic DNA markers (RFLP, SSLP, RAPD, SSN ); DNA probes,
Micro array studies and DNA chips and ORF analysis


Databases and analysis packages: Types of databases (Primary, secondary and
composite databases); Nucleic acid sequence databases, Protein sequence databases,
Prosite, Medline and Bibliographic databases (Pubmed, Agricola, Virtual library);
Specialized analysis packages: GCG, EGCG, Vector, NTI package, Mac Vector and
Synergy, Submission of sequences to databases

Structure databases: Protein Data Bank (PDB), Molecular Modeling Database,
CATH, SCOP and Visualizing structural information (RasMol, SPDB Viewer);
Prediction analysis of DNA sequences (GRAIL, FGENES, Genescan) and Sequence
alignment (FASTA, BLAST, CLUSTALW); Phylogenetic analysis: Distance method
and Neighbour-joining method; and Phylogenetic tree evaluation (PHYLIP)

Molecular docking and Protein ligand docking; Automated docking: Autodock and
Autogrid; Structure-based drug design and Virtual screening; Basic Lead
identification, Optimization, Validation and Identification of Lead compounds from
chemical libraries; De novo technique and Homology modeling; Pharmacophore
design, Force fields and energy minimization; QSAR- Hammett equation,


UNIX, C and Oracle: UNIX Operating System and Shell Programming; Programming
in C: Introduction, Basic data types in C, Control flow, Arrays, Functions, Storage
classes, Strings, Structures and Unions, Pointers; ORACLE: SQL (DBMS
introduction, Introduction of SQL, Data types, Data Definition, Manipulation and
control languages); PL/SQL (Introduction, Variables and data types, Conditional and
iterative statement, cursors); ADVANCED PL/SQL (Triggers, Procedures and

PERL: Introduction to PERL, data types & expressions, Subroutines; BIO-PERL:
Accessing sequence data from local and remote databanks and Accessories; Remote
Databases, Transforming sequence files and transforming alignment files, sequence
statistics, Identifying restriction enzyme sites and amino acid cleavage sites.

JAVA programming fundamentals: Introduction to Java, Decision making (Branching
and looping), JAVA classes and methods: Classes, Objects, Methods, Strings and
Vectors, JAVA inheritance: Applet programming, Graphics programming, Managing
Input/Output files in Java


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