Lovely Professional University,Punjab

Format For Instruction Plan [for Courses with Lectures and Labs

Course No BTY887

Cours Title FUNDAMENTALS OF BIOINFORMATICS

Course Planner 14803 :: Prashant Singh

Lectures Tutorial Practical Credits 3 0 0 3

Text Book:

1 Introduction to bioinformatics, Arthur M. Lesk, Third Edition, 2009.

Other Specific Book:

2 Lehninger Principles of Biochemistry, Nelson, Cox, 2007 3 Bioinformatics, Andreas D. Baxevanis, Francis Ouellette, 2006. 4 Introduction to bioinformatics, Attwood, 2008

Other Reading Sr No Jouranls atricles as compulsary readings (specific articles, Complete reference) 5 http://www.sinauer.com/pdf/Petsko_Ringe_contents.pdf 6 http://en.wikipedia.org/wiki/Protein 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 www.ncbi.nlm.nih.gov/ 9 www.pdb.org/ 10 http://bioinfo.ernet.in/s-star/downloads/tutorial/t1b.pdf Salient Features primary sequence database protein databank, a resource of protein structures overview of biological databases

11 http://bioinformatics.oxfordjournals.org/content/14/9/755.full.pd article of profile HMMs f+html 12 http://en.wikipedia.org/wiki/DNA 1 DNA Approved for Autumn Session 2011-12

13 http://en.wikipedia.org/wiki/RNA 14 http://en.wikipedia.org/wiki/Protein 15 http://en.wikipedia.org/wiki/DNA_replication 16 http://en.wikipedia.org/wiki/Transcription_%28genetics%29 17 http://en.wikipedia.org/wiki/Translation_%28biology%29

RNA Protein DNA Replication Transcription Translation

18 http://en.wikipedia.org/wiki/Reverse_transcription#Process_of Reverse Transcriptase _reverse_transcription

Detailed Plan For Lectures

Part 1
Week 1 Lecture 1 Lecture 2 Lecture 3 Week 2 Lecture 4 Basic Concepts: DNA Basic Concepts: RNA Basic Concepts: Proteins Sequence, Structure and function ->Reference :1,pg 6-9 ->Reference :1,pg 6-9 ->Reference :1,pg 6-9 ->Reference :1,pg 1114 ->Reference :1,pg 1114 ->Reference :1,pg 6-7 http://en.wikipedia.org/wi ki/DNA http://en.wikipedia.org/wi ki/RNA http://en.wikipedia.org/wi ki/Protein http://www.sinauer.com/ pdf/Petsko_Ringe_conte nts.pdf http://www.sinauer.com/ pdf/Petsko_Ringe_conte nts.pdf http://en.wikipedia.org/wi ki/Central_dogma_of_m olecular_biology http://en.wikipedia.org/wi ki/DNA_replication http://en.wikipedia.org/wi ki/DNA_replication http://en.wikipedia.org/wi ki/Transcription_ %28genetics%29 Approved for Autumn Session 2011-12

Lecture 5

Sequence, Structure and function

Lecture 6

Central dogma of molecular biology

Week 3

Lecture 7 Lecture 8 Lecture 9

Replication Replication Transcription

->Reference :15 ->Reference :15 ->Reference :16

Week 4

Lecture 10

Translation

->Reference :17

http//en.wikipedia.org/wi ki/Translation_ %28genetics%29

Part 2
Week 4 Lecture 11 Translation ->Reference :17 http//en.wikipedia.org/wi ki/Translation_ %28genetics%29 http://en.wikipedia.org/wi ki/Reverse_transcriptas e http://en.wikipedia.org/wi ki/Bioinformatics http://en.wikipedia.org/wi ki/Bioinformatics http://www.ebi.ac.uk/em bl/ http://www.ncbi.nlm.nih. gov/genbank/ http://www.ddbj.nig.ac.jp /

Lecture 12

Reverse Transcription

->Reference :18

Week 5

Lecture 13 Lecture 14 Lecture 15

Introduction to bioinformatics: history, objective and ->Reference :1,pg 2-5 application 12-15 Introduction to bioinformatics: history, objective and ->Reference :1,pg 2-5 application 12-15 Primary nucleotide sequence databases: EMBL Primary nucleotide sequence databases: GenBank Primary nucleotide sequence databases: DDBJ Protein sequence databases: SwissProt Protein sequence databases: SwissProt Protein sequence databases: TrEMBL ->Reference :1,pg 10 ->Reference :1,pg 10 ->Reference :1,pg 1011

Week 6

Lecture 16 Lecture 17 Lecture 18

->Reference :1,pg 156- http://expasy.org/sprot/ 161 193-197 ->Reference :1,pg 156- http://expasy.org/sprot/ 161 193-197 ->Reference :1,193194 ->Reference :1,pg 193194

Week 7

Lecture 19 Lecture 20

Lecture 21

Revision

MID-TERM Part 3
Week 8 Lecture 22 Lecture 23 Lecture 24 Sequence motif databases: Pfam Sequence motif databases: PROSITE Protein Structure Databases: PDB ->Reference :1,pg 198- http://en.wikipedia.org/wi 199 ki/Pfam ->Reference :1,pg 198- http://expasy.org/prosite/ 199 prosite_details.html ->Reference :1,pg 5152 199-203 http://www.pdb.org/pdb/ home/home.do

Approved for Autumn Session 2011-12

Week 9

Lecture 25 Lecture 26 Lecture 27

Protein Structure Databases: SCOP Protein Structure Databases: CATH Sequence alignment: Biological motivation Scoring matrix: PAM

->Reference :1,pg 204- http://scop.mrclmb. 205 cam.ac.uk/scop/ ->Reference :1,pg 204 http://www.cathdb.info/ pg 331 ->Reference :1,pg 243- http://en.wikipedia.org/wi 244 ki/Sequence_alignment ->Reference :1,pg 255- http://www.brc.dcs.gla.a 257 c.uk/~drg/courses/bioinf ormaticsHM/slides/scori ng_matrices.pdf

Week 10

Lecture 28

Part 4
Week 10 Lecture 29 Scoring matrix: BLOSUM ->Reference :1,pg 257- http://www.brc.dcs.gla.a 258 c.uk/~drg/courses/bioinf ormaticsHM/slides/scori ng_matrices.pdf ->Reference :1,pg 258- http://en.wikipedia.org/wi 259 ki/Gap_penalty ->Reference :1,pg 261- http://en.wikipedia.org/wi 266 ki/Needleman %E2%80%93Wunsch_a lgorithm ->Reference :1,pg 266- http://en.wikipedia.org/wi 267 ki/Smith %E2%80%93Waterman _algorithm ->Reference :1,pg 271- http://www.ebi.ac.uk/Too 273 pg 27-28 ls/msa/clustalw2/ ->Reference :1,pg 288- http://en.wikipedia.org/wi 290 ki/Neighbor_joining http://blast.ncbi.nlm.nih. gov/Blast.cgi http://www.ncbi.nlm.nih. gov/BLAST/tutorial/Altsc hul-1.html

Lecture 30 Week 11 Lecture 31

Gap Penalty Pairwise sequence alignment: Needleman Wunsch

Lecture 32

Pairwise sequence alignment: Smith Waterman

Lecture 33 Week 12 Lecture 34 Lecture 35

Multiple sequence alignment: ClustalW Phylogenetic analysis:NJ

Database Searching: BLAST, Statistics of sequence ->Reference :1,pg 259 alignment score: E-Value, PValue -261 ->Reference :1,pg 267270 Revision

Lecture 36

Approved for Autumn Session 2011-12

Spill Over
Week 13 Lecture 37 HMMs ->Reference :1,pg 278 http://en.wikipedia.org/wi -280 ki/Hidden_Markov_mod el ->Reference :1,pg 273 http://bioinformatics.oxfo -275 rdjournals.org/content/1 4/9/755.full.pdf+html

Lecture 38

Profiles

Details of homework and case studies

Class Test 1

To learn about Basic Concepts: DNA, RNA and Proteins basics concepts of Sequence, Structure and function biological sciences Central dogma of molecular biology Replication To learn about basics concepts of biological sciences and primary nucleotide sequence databases To learn about primary protein sequence and structural databases and scoring matrix for sequence alignment. Transcription Translation Reverse Transcription Introduction to bioinformatics: history, objective and application Primary nucleotide sequence databases: EMBL Primary nucleotide sequence databases: GenBank Primary nucleotide sequence databases: DDBJ Sequence motif databases: Pfam Sequence motif databases: PROSITE Protein Structure Databases: PDB Protein Structure Databases: SCOP Protein Structure Databases: CATH Sequence alignment: Biological motivation Scoring matrix: PAM Scoring matrix: BLOSUM

Based on class test performance.

Class Test 2

Individual

Based on class test performance.

6/6

Class Test 3

Individual

Based on class test performance.

10 / 10

Scheme for CA:out of 100*

Approved for Autumn Session 2011-12

Component Class Test

Frequency 2

Out Of 3 Total :-

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 Autumn Session 2011-12