Lovely Professional University,Punjab

Format For Instruction Plan [for Courses with Lectures and Labs

Course No BTY301T

Cours Title BASICS IN BIOINFORMATICS

Course Planner 13391 :: Nishtha Pandey

Lectures Tutorial Practical Credits 3 0 0 3

Text Book:

1 Bioinformatics: Principles and Applications, Zhumur Ghosh and Bibekanand Mallick, Oxford University Press, 2008

Other Specific Book:

2 Bioinformatics: Sequence and Genome Analysis, David W. Mount, Cold Spring Harbor Laboratory Press. Fifth Edition,(2005). 3 Biological sequence analysis: Probabilistic models of proteins and nucleic acids Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison, Cambridge University Press. Seventh Edition, (2002)

Other Reading Sr No Jouranls atricles as compulsary readings (specific articles, Complete reference) 4 Dennis A. Benson, Mark Boguski, David J. Lipman and James Ostell (1996), GenBank, Nucleic Acids Research, Vol. 24, No. 1 5 http://www.ncbi.nlm.nih.gov/RefSeq/GenBankvsRefSeq.pdf 6 Amos Bairoch and Rolf Apweiler (1997),The SWISS-PROT protein sequence data bank and its supplement TrEMBL, NAR, Vol. 25, No. 1 7 http://www.brc.dcs.gla.ac.uk/~drg/courses/bioinformaticsHM/slides/scoring_matrices.pdf Relevant Websites Sr. No. (Web adress) (only if relevant to the courses) 8 http://emboss.bioinformatics.nl/cgi-bin/emboss/dottup 9 http://swissmodel.expasy.org/course/text/chapter4b.htm 10 http://cib.cf.ocha.ac.jp/bitool/MIX/ 11 http://prowl.rockefeller.edu/aainfo/chou.htm 12 http://www.tutors4you.com/probabilitytutorial.htm 13 http://www.genome.jp/kegg/kegg1a.html 1 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 Approved for Spring Session 2011-12

14 http://pfam.sanger.ac.uk/ 15 http://www.yeastgenome.org/

About the Pfam database Resource for yeast genome

Detailed Plan For Lectures

Week Number Lecture Number Lecture Topic Chapters/Sections of Pedagogical tool Textbook/other Demonstration/case reference study/images/anmatio n ctc. planned

Part 1
Week 1 Lecture 1 Lecture 2 Lecture 3 Week 2 Lecture 4 Introduction to Bioinformatics Basics of probability Basics of probability GenBank ->Reference :1,Ch-1 314 ->Reference :12 ->Reference :12 ->Reference :1,Ch-4; 70-72 Online demonstration of database: http://www.ncbi.nlm.nih. gov/genbank/

Lecture 5 Lecture 6 Week 3 Lecture 7

GenBank RefSeq EMBL Bank, DDBJ

->Reference :1,Ch-4; 70-72 ->Reference :1,Ch-4; 74-75 ->Reference :1,Ch-4; 82-93 Online demonstration of database: http://www.ddbj.nig.ac.jp /

Lecture 8 Lecture 9

UniGene SwissProt, TrEMBL

->Reference :1,Ch-4; 73 ->Reference :1,Ch-4; 99-101 Online demonstration of database: http://www.ebi.ac.uk/uni prot/

Week 4

Lecture 10

PIR

->Reference :1,Ch-4; 94-99

Part 2
Week 4 2 Lecture 11 Pfam ->Reference :14 Approved for Spring Session 2011-12

Week 4

Lecture 12

PDB

->Reference :1,Ch-5; 103-110

Online demonstration of database: http://www.pdb.org/pdb/ home/home.do Online demonstration of database:http://www.ncb i.nlm.nih.gov/Structure/ MMDB/mmdb.shtml

Week 5

Lecture 13

MMDB

->Reference :1,Ch-5; 111-115

Lecture 14 Lecture 15 Week 6 Lecture 16

CATH SCOP KEGG OMIM, SGD

->Reference :1,Ch-5; 128-133 ->Reference :13 ->Reference :1,Ch 4 p Online demonstration of 82 database:http://www.ncb ->Reference :15 i.nlm.nih.gov/omim

Lecture 17 Lecture 18 Week 7 Lecture 19 Lecture 20 Lecture 21

Class Test PAM BLOSUM Jukes Cantor Revision ->Reference :1,Ch-6; 148-152 ->Reference :1,Ch-6; 153-158 ->Reference :1,Ch-8; 221

MID-TERM Part 3
Week 8 Lecture 22 Dotplot ->Reference :1,Ch6; 158-161 Online demonstration of tool:http://emboss.bioinf ormatics.nl/cgibin/emboss/dottup Online demonstration of tool:http://www.ebi.ac.uk /Tools/psa/emboss_nee dle/

Lecture 23

NW

->Reference :1,Ch6; 162-164

Lecture 24 Week 9 Lecture 25

NW,SW SW

->Reference :1,Ch6; 165-168 ->Reference :1,Ch6; 169-176 Online demonstration of tool:http://www.ebi.ac.uk /Tools/psa/

Approved for Spring Session 2011-12

Week 9

Lecture 26 Lecture 27

ClustalW ClustalW

->Reference :1,Ch6; 188-192 ->Reference :1,Ch6; 188-192 ->Reference :1,Ch8; 212-216 ->Reference :1,Ch8; 212-216 Online demonstration of tool:http://www.ebi.ac.uk /Tools/msa/clustalw2/

Week 10

Lecture 28 Lecture 29

Basics of phylogenetic studies and applications Basics of phylogenetic studies and applications

Part 4
Week 10 Lecture 30 BLAST ->Reference :1,Ch6; 182-186 ->Reference :1,Ch6; 182-186 ->Reference :1,Ch6; 178-181 ->Reference :1,Ch10; 278-281 ->Reference :1,Ch10; 278-281 ->Reference :1,Ch10; 281-282 ->Reference :1,Ch10; 284 ->Reference :1,Ch10; 295-306 ->Reference :1,Ch10; 295-306 Online demonstration of tool:http://cib.cf.ocha.ac. jp/bitool/MIX/ Online demonstration of tool:http://cib.cf.ocha.ac. jp/bitool/MIX/ Online demonstration of tool:http://blast.ncbi.nlm. nih.gov/Blast.cgi

Week 11

Lecture 31 Lecture 32 Lecture 33

BLAST FASTA Chou-Fasman Chou-Fasman

Week 12

Lecture 34

Lecture 35 Lecture 36

GOR GOR

Week 13

Lecture 37 Lecture 38 Lecture 39

Comparative modelling Comparative modelling Revision

Spill Over
Week 14 Lecture 40 Lecture 41 RasMol DeepView ->Reference :1,250258 ->Reference :1,250258 Approved for Spring Session 2011-12

Details of homework and case studies

Homework No. Objective Topic of the Homework Nature of homework (group/individuals/field work Evaluation Mode Allottment / submission Week 2/4

Homework 1

To direct students Problems on basics of probability, random probability, conditional Individual to worthwhile probability. practice at home 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. Individual

Effort put in by the student.

Test 1

Performance in test

6/6

Case study 1

To check Case study topics for developing their analytical skills and to understanding and understand application of bioinformatics tools expression skills of students.

Group

analysis skills and presentation

8 / 10

Scheme for CA:out of 100*

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

* In ENG courses wherever the total exceeds 100, consider x best out of y components of CA, as explained in teacher's guide available on the UMS

Approved for Spring Session 2011-12