Course Curriculam

Course Code: BIOF202 Credit Units L T P/S SW AS/DS FW No. of PSDA Total Credit Unit
Course Level UG 2 0 2 2 0 0 0 4
Course Title Basic Bioinformatics

Course The course is designed for the understanding of biological databases, sequence and structural analysis of the biological data.
Description :

Course Objectives :

SN
Objectives
.
Theory: The basic objective is to give students an introduction to the basic practical techniques of bioinformatics. Emphasis will be given to the
1 application of bioinformatics and biological databases to problem solving in real research problems. The students will become familiar with the use of
a wide variety of internet applications, biological database and will be able to apply these methods to research problems.
Practical: The aim is to provide practical training in bioinformatics methods including accessing the major public sequence databases, use of the
different computational tools to find sequences, analysis of protein and nucleic acid sequences by various software packages. It also provides a step
2
by step, theoretical and practical introduction to the development of useful tools for automation of complex computer jobs, and making these tools
accessible on the network from a Web browser.

Pre-Requisites : General

SN. Course Code Course Name

Course Contents / Syllabus :

SN. Module Descriptors / Topics Weightage

Introduction
to Definition and History and Applications of Bioinformatics, Internet resources, various databases and bioinformatics
1 25.00
Bioinformatic tools, organization of databases
s
Nucleic acid sequence databases, Protein sequence databases, Repositories for high throughput genomic
Biological
2 sequences, Genome Databases, 3D Structure Database, Chemical Structure database, Gene Expression database, 25.00
Databases
Derived Databases, Structure classification database, Protein-Protein interaction database and Pathway databases.
File formats, Basic concepts of sequence analysis, Scoring matrices, Pair wise sequence alignments, Multiple
Sequence
3 sequence alignment, Database Searches: Keyword-based searches and Sequence-based searches, Profile-based 25.00
Analysis
searches, Markov chains and applications
Overview and Introduction to Protein Structure, Sequence-Sequence Alignment Methods, Sequence Based
Structure Secondary Structure Prediction. Visualization of structures using Rasmol or SPDBV. Fundamentals of the methods
4 25.00
Prediction for 3D structure prediction, Homology/comparative Modeling, fold recognition, threading approaches, and ab initio
structure prediction methods. Use of modeller.

Course Learning Outcomes :

SN. Course Learning Outcomes

The students will be able to describe the contents and properties of the most important bioinformatics databases, perform text- and sequence-
1
based searches, and analyze and discuss the results in light of molecular biological knowledge.
The students will be able to explain the major steps in pairwise and multiple sequence alignment, explain the principle for, and execute pairwise
2
sequence alignment by dynamic programming.
3 The students will be able to predict the secondary and tertiary structures of protein sequences.
4 Design integrated assignment using various biological databases,sequence alignment technoiques and protein structure prediction.

Pedagogy for Course Delivery :

SN. Pedagogy Methods

1 Lectures:26
2 Presentation:2
3 Class Test:2
4 Practical:28
5 Lab internal:2

Theory /VAC / Architecture Assessment (L,T & Self Work): 75.00 Max : 100

Attendance+CE+EE : 5+45+50

SN. Type Component Name Marks

1 Attendance 5.00
2 End Term Examination (OMR) 50.00
3 Internal CLASS TEST 20.00
4 Internal INTEGRATED ASSIGNMENT 20.00
5 Internal PRESENTATION 5.00

Lab/ Practical/ Studio/Arch. Studio/ Field Work Assessment : 25.00 Max : 100

Attendance+CE+EE : 5+45+50

SN. Type Component Name Marks

1 Attendance 5.00
2 External REPORT 10.00
3 External PRACTICAL 25.00
4 External VIVA VOCE 15.00
5 Internal VIVA VOCE 15.00
6 Internal CLASS TEST (PRACTICAL BASED) 20.00
7 Internal PRACTICAL / LAB RECORDS 10.00

Lab/ Practical details, if applicable :

SN. Lab / Practical Details

1 Referencing in Scientific literature and their practical usage, PubMed.
2 Sequence retrieval.
3 Pair wise sequence alignment.
4 Biological Databases: Study of different Biological databases (esp. the ones given below), Format.
5 Local and Global alignment – Algorithms.
6 DOT matrix analysis
7 Databases search for homologous sequence using (BLAST) and (FASTA).
8 MSA: (Clustal W, Clustal X, PILE UP), Algorithms-MSA, Progressive alignment etc, Problems with MSA method, Statistics behind MSA.
9 Protein structure prediction tools.

List of Professional skill development activities :

[Link] PSDA : 0
SN. PSDA Point

Text & References :

SN. Type Title/Name Description ISBN/ URL

David W Mount, Bioinformatics- Sequence
1 Book and genome analysis , Cold Spring Harbor 978-0879697129
Laboratory Press.
• Bioinformatics: A Practical Guide to the
2 Book 978-0471478782
Analysis of Genes and Proteins.
• Bioinformatics: Sequence, Structure and ISBN: 978-
3 Book
Databanks: A Practical Approach. 0199637904
• Introduction to Bioinformatics, Teresa ISBN: 978-
4 Book
Attwood, David Parry-Smith. 8178085074