UNIVERSITY OF KERALA - Marian Engineering College

B.Tech Comp. Sc. & Engg., University of Kerala 88
08.806 (5) BIOINFORMATICS (ELECTIVE IV) 3 – 1 – 0
Module I (17 hours)
Introduction to Life Sciences: Levels of organization in nature: atom, molecule, organelle, cell, tissue, organ,
organ system; Unicellular and multicellular organisms; Branches of Biology - Cell Biology - Cell as the
structural and functional unit of life - Structural components of cell - Types of cells - Prokaryotic, Eukaryotic,
Animal and Plant cell; Important Biomolecules- Nuclei acids, proteins, enzymes.
Central Dogma: DNA, RNA and Protein; Chromosome, Genome, Genes, Gene Loci, Gene Sequencing –
Short gun and Contig approach; Restriction Enzyme, restriction sites, DNA copying/amplification, PCR and
Electrophoresis.
Module II (18 hours)
Genomics & Proteomics: String view of DNA, Reading Frames (+1, +2, +3, -1, -2, -3), Open reading frame,
codon, genetic code, transcription & translation- mRNA, sense and anti-sense strands, rRNA, tRNA,
upstream and downstream, genomic DNA, complimentary DNA, introns and exons, alternative spicing, junk
DNA, Sequence databases- GenBank, EMBL and DDBJ- concepts of similarity- homologous- orthologous
and paralogous sequences, FASTA file format.
Sequence alignments- need for alignment - local and global alignments – pair-wise and multiple – PAM and
BLOSSUM matrices – Needleman–Wunch and Smith-Waterman algorithms – Study on BLAST results. Gene
structure – typical prokaryotic and eukaryotic gene structures – Single Nucleotide Polymorphisms (SNPs);
Concepts of Phylogenetics, Distance based methods to draw phylogenetic trees – UPGMA and NJ algorithm.
Study of ClustalW/ClustalX, Phylip and NJ Plot software.
Proteome and proteomics – proteins as workhorse molecules of life; protein separation using 2D gel
electrophoresis; Study on amino acids and four levels of protein structure – Protein databases – PDB, Uniprot
Module III (17 hours)
Basics of Computer Aided Drug Design (CADD), Microarray Bioinformatics, Synthetic Biology and Systems
Biology. Soft computing methods in Bioinformatics – Basics of Hidden Markov Models, Artificial Neural
Networks, Genetic Algorithms and Ant Colony Optimization.
Text Books:
1. Essential Biology (Abridged) Campbell, Cambridge
2. Fundamental Concepts of Bioinformatics – D. E. Krane and M. L. Raymer, Pearson education
Reference Books:
1. Bioinformatics: Sequence & Genome Analysis – D. Mount, Cold Spring Harbor press, USA (Indian edition)
2. Microarray Bioinformatics – D. Stekel, Cambridge University Press (Indian Edition)
3. Computer Aided Drug Design: Methods and Applications – (Edited) T. J Perun, C. L Propst, Marcel Dekker.
4. Systems Biology & Synthetic Biology – Pengcheng Fu and Syen Panke, Wiley.
5. www. Wikipedia – Soft computing methods (refer study materials for)
Internal Continuous Assessment (Maximum Marks-50)
25 Marks - Tests (minimum 2)
15 Marks - Assignments (minimum 3) such as home work, problem solving, literature survey, seminar,
term-project, software exercises, etc.
10 Marks - Regularity in the class
University Examination Pattern
PART A: Short answer questions 10 x 4 marks=40 marks
All questions are compulsory. There should be at least three questions
from each module and not more than four questions from any module.
PART B: Descriptive/Analytical/Problem solving questions 3 x 20 marks=60 marks
Candidates have to answer one question out of two or two questions
out of four from each module.
Maximum Total Marks: 100