Course code Course title L T P J C

BIT1029 BASIC BIOINFORMATICS 3 0 0 0 3

Pre-requisite NONE Syllabus version
v.1.0
Course Objectives:
 The students would be able to understand and explain the fundamentals of Bio‐
informatics, Dynamic programming, searching algorithms, Evolutionary trees, DNA
mapping, DNA sequencing and Gene predictions

Expected Course Outcome:

 Students will interpret relationships among living things and analyze and solve biological
problems, from the molecular to ecosystem level using basic biological concepts, grounded
in foundational theories.

Student Learning Outcomes (SLO): 1,2,5

 knowledge and awareness of the basic principles and concepts of biology, computer sci-
ence and mathematics
 existing software effectively to extract information from large databases and to use this in-
formation in computer modelling

 problem-solving skills, including the ability to develop new algorithms and analysis meth-
ods an understanding of the intersection of life and information sciences, the core of shared
concepts, language and skills the ability to speak the language of structure-function rela-
tionships, information theory, gene expression, and database queries 
Module:1 Introduction to Bioinformatics 6 Hours SLO: 1,2
Scope of Bioinformatics – Elementary commands and Protocols, ftp, telnet, http, Primer on
information theory.

Module:2 Sequencing Alignment and Dynamic 6 Hours SLO: 1,2

Programming
Introduction – Strings – Edit distance between two strings – string similarity local alignment gaps
–Parametric sequence alignments – multiples alignment – common multiple alignment methods.

Module:3 Sequence Databases and Uses 6 Hours SLO: 5

Introduction to databases – database search – Algorithms issues in database search – sequence
database search – FASTA – BLAST – Amino acid substitution matrices PAM AND BLOSSUM

Module:4 Evolutionary Trees and Phylogeny 6 Hours SLO: 5

Ultrasonic trees – parsimony – Ultrametric problem – Perfect phylogeny – Phylogenetic alignment
–connection between multiple alignment and tree construction

Module:5 Special Topics in Bioinformatics 6 Hours SLO: 1,5

DNA Mapping and sequencing – Map alignment – Large scale sequencing and alignment –
shotgun –DNA sequencing – sequence assembly – Gene predictions – Molecular predictions with
DNA strings

Module:6 Strings and Evolutionary Trees 6 hours SLO: 2,5

Ultrametric trees and ultrametric distances - Additive-distance trees - Parsimony: charac ter-
based evolutionary reconstruction - The centrality of the ultrametric problem - Maximum
parsimony, Steiner trees, and perfect phylogeny Phylogenetic alignment, again - Connections
between multiple alignment and tree construction

Module:7 Matching DNA to protein 6 hours SLO: 2,5

Matching DNA to protein with frameshift errors - Gene prediction - Molecular computation:
computing with DNA strings

Module:8 Contemporary issues: Genome-Level Mutations 3 hours -

Total Lecture hours: 45 hours

Text Book(s)
1. Dan Gusfield,(1997)"Algorithms On Strings Trees and Sequences", Cambridge University
Press
Reference Books
1. Westhead, "Instant notes – Bioinformatics", Viva Publishers. 2.Bergeron Bryan,
"Bioinformatics Computing", Prentice Hall of India

Recommended by Board of Studies 15-12-2015

Approved by Academic Council No. 39 Date 15-12-2015