GENETIC ENGINEERING L T P C 3 0 0 3 OBJECTIVES:  To discuss the gene cloning methods and the tools and techniques

involved in gene cloning and genome analysis and genomics.  To explain the heterologous expression of cloned genes in
different hosts.

UNIT I: BASICS OF RECOMBINANT DNA TECHNOLOGY

Manipulation of DNA – Restriction and Modification enzymes, Design of linkers and adaptors. Characteristics of cloning and
expression vectors based on plasmid and bacteriophage, Vectors for insect, yeast and mammalian system, Prokaryotic and
eukaryotic host systems, Introduction of recombinant DNA in to host cells and selection methods.

UNIT II: DNA LIBRARIES

Construction of genomic and cDNA libraries, Artificial chromosomes – BACs and YACs, Chromosomal walking, Screening of
DNA libraries using nucleic acid probes and antisera.

UNIT III: SEQUENCING AND AMPLIFICATION OF DNA

Maxam Gilbert’s and Sanger’s methods of DNA sequencing. Inverse PCR, Nested PCR, AFLPPCR, Allele specific PCR,
Assembly PCR, Asymmetric PCR, Hot start PCR, inverse PCR, Colony PCR, single cell PCR, Real-time PCR/qPCR – SYBR green
assay, Taqman assay, Molecular beacons. Site directed mutagenesis.

UNIT IV: ORGANIZATION AND STRUCTURE OF GENOMES

Organization and structure of genomes, Genome sequencing methods, Conventional and shotgun genome sequencing
methods, Next generation sequencing technologies , Ordering the genome sequence, Genetic maps and Physical maps, STS
content based mapping, Restriction Enzyme Finger Printing, Hybridization mapping, Radiation Hybrid Maps, Optical
mapping. ORF finding and functional annotation.

UNIT V: CURRENT STATUS OF GENOME SEQUENCING PROJECTS

Current status of genome sequencing projects, Introduction to Functional genomics, Microarrays, Serial Analysis of Gene
expression (SAGE), Subtractive hybridization, DIGE, TOGA, Yeast Two hybrid System, Comparative Genomics,
Proteogenomics, Web resources for Genomics, Applications of genome analysis and genomics.

TOTAL: 60 PERIODS

BT3601 BIOINFORMATICS L T P C 3 0 0 3

OBJECTIVES:  To launch the Bioinformatics core concepts to students.  To provide knowledge on Biological databases,
sequence analysis,evolutionary analysis and applications of Bioinformatics.

UNIT I BIOLOGICAL DATABASES:

Introduction to Bioinformatics and Computational Biology, Biological sequences, Classification of biological databases -
Sequence Databases, Structure Databases, Genome specific databases, Special Databases and applications- Microarray,
Metabolic pathway, motif, and domain databases, Data file formats.

UNIT II SEQUENCE ANALYSIS:

Sequence Alignment- Homology vs Similarity, Similarity vs Identity. Types of Sequence alignment - Pairwise and Multiple
sequence alignment, Global alignment, Local alignment, Dotplot, Alignment algorithms- Needleman wunsch and Smith and
waterman algorithm, Substitution matrices- PAM, 94 BLOSUM.Multiple Sequence Alignment- Application of multiple
alignments, Viewing and editing of MSA and Scoring function.Database Similarity Searching- Basic Local Alignment Search
Tool (BLAST), FASTA, PHI BLAST, PSI BLAST, BLAST algorithm.

UNIT III MOLECULAR PHYLOGENY:

Phylogenetics Basics, Molecular clock theory, Ultrametric trees, Distance matrix methodsUPGMA,NJ, Character based
methods-Maximum Parsimony. Methods of evaluating phylogenetic methods- boot strapping, jackknifing.
UNIT IV MACROMOLECULAR STRUCTURE ANALYSIS:

Gene prediction, Conserved domain analysis, Protein structure visualization, Prediction of protein secondary structure,
Tertiary structure prediction- Homology modeling, Threading, Ab-initio prediction. Validation of the predicted structure
using Ramachandran plot, steriochemical properties, Structure- structure alignment.

UNIT V APPLICATIONS: Introduction to Systems Biology and Synthetic Biology, Microarray data analysis, DNA computing,
Bioinformatics approaches for drug discovery, Applications of Bioinformatics in genomics and proteomics- Assembling the
genome, STS content mapping for clone contigs, Functional annotation, Peptide mass fingerprinting.

TOTAL: 45 Periods

BT3611 BIOINFORMATICS LAB L T P C 0 0 3 1.5

Objectives  To provide a practical exposure to the bioinformatics databases, tools and software.  To select and use
functions in Perl for processing sequence data.

LIST OF EXPERIMENTS

1. Introduction to UNIX basic commands.

2. Perl programming and applications to Bioinformatics.  Basic scripting.  Regular expression96  File i/o& control
statement.  Subroutines  String specific functions.

3. Biological databases and their uses  Sequence databases  Structure databases

4. Sequence Analysis  BLAST, FASTA  Multiple sequence alignment  ExPASy Tools  DOTPLOT

5. Phylogenetic tree prediction

6. Protein secondary structure prediction

7. Protein tertiary structure prediction- Homology modeling using automated tool and Any open source software.

8. Lead molecule search using databases.

9. Protein-Ligand docking

10. Protein-Protein docking

11. ADMET modeling

12. Gene prediction tools.

TOTAL : 45 PERIODS

BT3511 MOLECULAR BIOLOG AND GENETIC ENGINEERING L T P C LABORATORY 0 0 4 2

COURSE OBJECTIVES:  Provide hands-on experience in performing basic molecular biology and Genetic Engineering
techniques.  Introduce the theory behind in each technique and to describe common applications of each methodology in
biological research. This will facilitate the students to take up specialized project in Molecular biology and will be a pre-
requisite for research work.

LIST OF EXPERIMENTS

1. Isolation of total DNA

2. Isolation of Plasmid DNA

3. Agarose gel electrophoresis

4. Restriction enzyme digestion of DNA

5. DNA ligation
6. Competent cell preparation & Transformation

7. Blue-White screening

8. Induction and Analysis of Gene expression

9. PCR

10. SDS-PAGE

11. Western blot