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
- Gain knowledge on Bioinformatics and different applications in computer Science
Course Outcomes
Knowledge on Computer applications in Bioinformatics
Essential Reading
- Krane D E, Fundamental Concepts of Bioinformatics, Pearson , 2003
- Rastogi S. C., Bioinformatics: Methods and Applications: Genomics, Proteomics and Drug Discovery, PHI , 2013
Supplementary Reading
- S. C. Rastogi, Bioinformatics Concepts, Skills and Applications, CBS , 2009
- Ghosh, Z, Bioinformatics: Principles and Applications, OUP , 2008
Journal and Conferences
- Epert systems and KDD
- 2. Journal: Journal of system software, 2. Conference: Software engineering and knowledge engineering