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Documente Profesional
Documente Cultură
Format For Instruction Plan [for Courses with Lectures and Labs
Course No BTY887
Text 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
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
Lecture 6
Week 3
Week 4
Lecture 10
Translation
->Reference :17
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
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
->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
Week 9
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 32
Database Searching: BLAST, Statistics of sequence ->Reference :1,pg 259 alignment score: E-Value, PValue -261 ->Reference :1,pg 267270 Revision
Lecture 36
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
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
Class Test 2
Individual
6/6
Class Test 3
Individual
10 / 10
Frequency 2
Out Of 3 Total :-
* 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