Course Details

Subject {L-T-P / C} : CS6415 : Bioinformatics { 3-0-0 / 3}

Subject Nature : Theory

Coordinator : Prof. Sambit Bakshi

Syllabus

Unit 1. LIFE - At its simplest:
Cellular Architecture, Nucleic Acids (RNA & DNA ), DNA replication, Repair and recombination. Transcription, Genetic code, Gene expression, Protein structure and function, Molecular biology tools.Biological databases, Statistical Methods: Estimation, Hypothesis testing, Random Walks, Markov Models.
Unit 2. Suffix Trees:
Exact & Approximate string matching, suffix tree introduction, properties, construction, problems with example, implicit suffix tree, brute force algorithm, Ukkonen algorithm with extension rules, Suffix link, skip & count trick, edge compression,
Generalised suffix tree, Exact string,Longest common substring, DNA contamination, Suffix array
Unit 3. Inexact matching, sequence alignment, dynamic programming, weighted edit distance,string similarity, local alignment, gaps, Pair wise sequence alignment (local), Multiple String Alignments :
Need of MSA, Family & Super Family representation, multiple sequence comparison
for structural inferences, Multiple alignments with sum-of- pairs, consensus objective functions.
Unit 4. Sequencing
Fragment Assembly (Shortest common super string algorithms based on multi-graph),
Sequencing by Hybridization, Protein sequencing.
Unit 5. Database searching for similar sequence (FASTA, BLAST), PAM, BLOSOM substitution matrices.Introduction to Motif Prediction, Gene prediction, Protein structure Prediction.

Course Objectives

Course Outcomes

Knowledge on Computer applications in Bioinformatics

Essential Reading

Supplementary Reading

Journal and Conferences