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Lovely Professional University, Punjab

Course Code BTY301T Course Category Course Title BASICS IN BIOINFORMATICS Courses with conceptual focus Course Planner 14664::Vikas Kaushik Lectures 3.0 Tutorials Practicals Credits 0.0 0.0 3.0

TextBooks Sr No T-1 Title Bioinformatics: Principles and Applications Reference Books Sr No R-1 R-2 Title Bioinformatics: Sequence and Genome Analysis Biological sequence analysis: Probabilistic models of proteins and nucleic acids Author David W. Mount Richard Durbin Edition 5th 7th Year Publisher Name Cold spring harbor Cambridge Univ Press Author Zhumur Ghosh and Bibekanand Mallick Edition 1st Year 2008 Publisher Name Oxford University Press

Other Reading Sr No OR-1 OR-2 OR-3 OR-4 OR-5 Journals articles as Compulsary reading (specific articles, complete reference) Dennis A. Benson, Mark Boguski, David J. Lipman and James Ostell (1996), GenBank, Nucleic Acids Research, Vol. 24, No. 1 , http://www.ncbi.nlm.nih.gov/RefSeq/GenBankvsRefSeq.pdf , Amos Bairoch and Rolf Apweiler (1997),The SWISS-PROT protein sequence data bank and its supplement TrEMBL, NAR, Vol. 25, No. 1 , http://www.brc.dcs.gla.ac.uk/~drg/courses/bioinformaticsHM/slides/scoring_matrices.pdf , Essential Bioinformatics from Xin Xiong ,Cambridge university press ,2008 ,

Relevant Websites Sr No RW-1 RW-2 RW-3 RW-4 RW-5 RW-6 (Web address) (only if relevant to the course) http://emboss.bioinformatics.nl/cgi-bin/emboss/dottup http://swissmodel.expasy.org/course/text/chapter4b.htm http://cib.cf.ocha.ac.jp/bitool/MIX/ http://prowl.rockefeller.edu/aainfo/chou.htm http://www.tutors4you.com/probabilitytutorial.htm http://www.genome.jp/kegg/kegg1a.html Salient Features Online tool to demonstrate working of dotplot Resource for structural classification of proteins Online tool for sequence alignment Resource for secondary structure prediction algorithm Basics of probability About KEGG

LTP week distribution: (LTP Weeks) Weeks before MTE Weeks After MTE Spill Over 7 6 2

Detailed Plan For Lectures


Week Number Lecture Number Broad Topic(Sub Topic) Chapters/Sections of Text/reference books Other Readings, Lecture Description Relevant Websites, Audio Visual Aids, software and Virtual Labs OR-5 General outline of the course Learning Outcomes Pedagogical Tool Demonstration/ Case Study / Images / animation / ppt etc. Planned

Week 1

Lecture 1

Introduction to Bioinformatics (Major Bioinformatics Resources)

T-1:Ch-1

Students having gained Slides bioinformatics skills and knowledge can secure employment or advance toward higher education in bioinformaticsrelated disciplines Understand the latest advances in bioinformatics representation of Biological data Slides

Lecture 2

Introduction to Bioinformatics (Open access Resources)

T-1:Ch-1

Understand the topic so that be able to identify and pursue research on this topic Understand the topic so that be able to identify and pursue research on this topic Understand the topic so that be able to identify and pursue research on this topic Understand the topic so that be able to identify and pursue research on this topic RW-5 Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work

Lecture 3

Introduction to Bioinformatics(File formats)

T-1:Ch-2

Slides

Week 2

Lecture 4

Introduction to Bioinformatics (Applications of Bioinformatics)

T-1:Ch-1

Understand the latest advances in bioinformatics Understand the latest advances in bioinformatics Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis

Slides

Lecture 5

Introduction to Bioinformatics (Computational Biology)

T-1:Ch-1

Slides

Lecture 6

Introduction to Bioinformatics (Basics of Probability)

Slides

Week 3

Lecture 7

Introduction to Bioinformatics (Basics of Probability)

RW-5

Slides

Week 3

Lecture 8

Nucleotide sequence database (Genebank)

T-1:Ch-4

Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work

Set a solid background Slides in bioinformatics

Lecture 9

Nucleotide sequence database (EMBL)

T-1:Ch-4

Set a solid background Slides in bioinformatics

Week 4

Lecture 10

Nucleotide sequence database (DDBJ)

T-1:Ch-4

Set a solid background Slides in bioinformatics

Nucleotide sequence database (UniGene)

T-1:Ch-4

Set a solid background Slides in bioinformatics

Nucleotide sequence database (RefSeq)

T-1:Ch-4

Set a solid background Slides in bioinformatics

Lecture 11

Protein sequence resource (SwissProt)

T-1:Ch-4

Set a solid background Slides in bioinformatics

Lecture 12

Protein sequence resource (TrEMBL)

T-1:Ch-4

Set a solid background Slides in bioinformatics

Protein sequence resource(Pfam)

T-1:Ch-4

Set a solid background Slides in bioinformatics

Week 5

Lecture 13

Protein sequence resource(PIR)

T-1:Ch-4

Set a solid background Slides in bioinformatics

Lecture 14

Protein structure resource and other relevant database(PDB & MMDB) Protein structure resource and other relevant database(PDB & MMDB) Protein structure resource and other relevant database(SCOP & CATH)

T-1:Ch-5

Set a solid background Slides in bioinformatics

Lecture 15

T-1:Ch-5

Set a solid background Slides in bioinformatics

Week 6

Lecture 16

T-1:Ch-5

Set a solid background Slides in bioinformatics

Week 6

Lecture 17

Protein structure resource and other relevant database(KEGG, OMIM & SGD)

RW-6

Understand the topic so that be able to use this topic in the industry realted work Homework,Test,Case study 2

Set a solid background Slides in bioinformatics

Lecture 18 Week 7 Lecture 19 Substitution matrices(Jukes Cantor) T-1:Ch-6

Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work

Set a solid background Slides in bioinformatics

Substitution matrices(PAM)

T-1:Ch-6

Set a solid background Slides in bioinformatics

Lecture 20

Substitution matrices(BLOSUM)

T-1:Ch-6

Set a solid background Slides in bioinformatics

Lecture 21

Substitution matrices(BLOSUM)

T-1:Ch-6

Set a solid background Slides in bioinformatics

MID-TERM
Week 8 Lecture 22 Pairwise sequence alignment (Dotplot) T-1:Ch-6 Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis Slides

Lecture 23

Pairwise sequence alignment (Global Alignment)

T-1:Ch-6

Slides

Lecture 24

Pairwise sequence alignment (Global Alignment)

T-1:Ch-6

Slides

Week 9

Lecture 25

Pairwise sequence alignment (Local Alignment)

T-1:Ch-6

Slides

Lecture 26

Multiple sequence alignment (Progressive Method-- clustalw)

T-1:Ch-6

Slides

Week 9

Lecture 27

Multiple sequence alignment (Progressive Method-- clustalw)

T-1:Ch-6

Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work

Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis Master the computational techniques for biological sequence analysis

Slides

Week 10

Lecture 28

Multiple sequence alignment (Heuristic Method)

T-1:Ch-6

Slides

Lecture 29

Basics of phylogenetic studies and applications(Distance based Method)

T-1:Ch-8

Slides

Lecture 30

Basics of phylogenetic studies and applications(Distance based Method)

T-1:Ch-8

Slides

Week 11

Lecture 31

Basics of phylogenetic studies and applications(Charactor Based method)

T-1:Ch-8

Slides

Lecture 32

Sequence based database search (BLAST)

T-1:Ch-6

Slides

Lecture 33

Sequence based database search (FASTA)

T-1:Ch-6

Slides

Sequence based database search (PSI- BLAST)

T-1:Ch-6

Slides

Week 12

Lecture 34

Structure prediction of proteins (Chou-Fasman & GOR Method)

T-1:Ch-10

Familiar with structure Slides Prediction Methods

Lecture 35

Structure prediction of proteins (Chou-Fasman & GOR Method)

T-1:Ch-10

Familiar with structure Slides Prediction Methods

Week 12

Lecture 36

Structure prediction of proteins (Chou-Fasman & GOR Method)

T-1:Ch-10

Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work Understand the topic so that be able to use this topic in the industry realted work

Familiar with structure Slides Prediction Methods

Week 13

Lecture 37

Structure prediction of proteins (Comparative modeling)

T-1:Ch10

Familiar with structure Slides Prediction Methods

Lecture 38

Structure prediction of proteins (Comparative modeling)

T-1:Ch10

Familiar with structure Slides Prediction Methods

Lecture 39

Structure prediction of proteins (Comparative modeling)

T-1:Ch10

Familiar with structure Slides Prediction Methods

SPILL OVER
Week 14 Lecture 40 R-1:Ch-1 OR-5 ANN Understand the latest advances in bioinformatics Understand the latest advances in bioinformatics Slides

Lecture 41

R-1:Ch-1

OR-5

HMM

Slides

Scheme for CA:


Component Homework,Test,Case study Frequency 2 Total :Out Of 3 Each Marks Total Marks 10 10 20 20

Details of Academic Task(s)


AT No. Objective Topic of the Academic Task Nature of Academic Task (group/individuals/field work Individual Evaluation Mode Allottment / submission Week 2/4

Homework 1

To direct students to Problems on basics of probability, random probability, worthwhile practice conditional at home probability. Organization of NCBI, INSDC. GenBank versus RefSeq To evaluate the students on the basis of their attentiveness in class Application based questions from EMBL Bank, DDBJ, Protein sequence and structure resources.

Effort put in by the student.

Test 1

Individual

Performance in test

6/6

Case study 1

To check understanding and expression skills of students.

Case study topics for developing their analytical skills and to understand application of bioinformatics tools

Group

Analysis skills and presentation

8 / 11

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