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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
Week 1
Lecture 1
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
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
T-1:Ch-2
Slides
Week 2
Lecture 4
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
T-1:Ch-1
Slides
Lecture 6
Slides
Week 3
Lecture 7
RW-5
Slides
Week 3
Lecture 8
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
Lecture 9
T-1:Ch-4
Week 4
Lecture 10
T-1:Ch-4
T-1:Ch-4
T-1:Ch-4
Lecture 11
T-1:Ch-4
Lecture 12
T-1:Ch-4
T-1:Ch-4
Week 5
Lecture 13
T-1:Ch-4
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
Lecture 15
T-1:Ch-5
Week 6
Lecture 16
T-1:Ch-5
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
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
Substitution matrices(PAM)
T-1:Ch-6
Lecture 20
Substitution matrices(BLOSUM)
T-1:Ch-6
Lecture 21
Substitution matrices(BLOSUM)
T-1:Ch-6
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
T-1:Ch-6
Slides
Lecture 24
T-1:Ch-6
Slides
Week 9
Lecture 25
T-1:Ch-6
Slides
Lecture 26
T-1:Ch-6
Slides
Week 9
Lecture 27
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
T-1:Ch-6
Slides
Lecture 29
T-1:Ch-8
Slides
Lecture 30
T-1:Ch-8
Slides
Week 11
Lecture 31
T-1:Ch-8
Slides
Lecture 32
T-1:Ch-6
Slides
Lecture 33
T-1:Ch-6
Slides
T-1:Ch-6
Slides
Week 12
Lecture 34
T-1:Ch-10
Lecture 35
T-1:Ch-10
Week 12
Lecture 36
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
Week 13
Lecture 37
T-1:Ch10
Lecture 38
T-1:Ch10
Lecture 39
T-1:Ch10
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
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.
Test 1
Individual
Performance in test
6/6
Case study 1
Case study topics for developing their analytical skills and to understand application of bioinformatics tools
Group
8 / 11