BT 9212 COMPUTATIONAL BIOLOGY SYLLABUS | ANNA UNIVERSITY MTECH BIOTECHNOLOGY 1ST SEM SYLLABUS REGULATION 2009 2011 2012-2013 BELOW IS THE ANNA UNIVERSITY FIRST SEMESTER M.TECH BIOTECHNOLOGY DEPARTMENT SYLLABUS, TEXTBOOKS, REFERENCE BOOKS,EXAM PORTIONS,QUESTION BANK,PREVIOUS YEAR QUESTION PAPERS,MODEL QUESTION PAPERS, CLASS NOTES, IMPORTANT 2 MARKS, 8 MARKS, 16 MARKS TOPICS. IT IS APPLICABLE FOR ALL STUDENTS ADMITTED IN THE YEAR 2011 2012-2013 (ANNA UNIVERSITY CHENNAI,TRICHY,MADURAI, TIRUNELVELI,COIMBATORE), 2009 REGULATION OF ANNA UNIVERSITY CHENNAI AND STUDENTS ADMITTED IN ANNA UNIVERSITY CHENNAI DURING 2009
BT 9212 COMPUTATIONAL BIOLOGY L T P C
2 0 2 3
UNIT I INTRODUCTION TO COMPUTATIONAL BIOLOGY 7
Molecular sequences. Sequence analysis. Dynamic programming. Pairwise and multiple
sequence alignment and motifs. Applications.
UNIT II DATABASES 6
Scoring matrices, heuristic methods of database searching: BLAST family of programs,
FASTA. Phylogenetic trees.
UNIT III INTRODUCTION TO GENOMICS AND PROTEOMICS 10
Functional, structural and comparative genomics. Gene finding and annotation. Protein
structure. Homology modeling. Differential gene expression.
UNIT IV MACHINE LEARNING TECHNIQUES 12
Hidden Markov models, Neural nets, Decision trees and their application in
computational biology. Eukaryotic and prokaryotic gene finding. DNA Computing.
UNIT V INTRODUCTION TO PERL 10
Variables, Data types, control flow constructs, arrays, lists and hashes, String
manipulation, File handling.
LAB:
Sequence analysis : Pairwise and multiple sequence alignment. Tools available
for sequence analysis. Motif generation.
Databases : Exploring biological databases
Database searching : Using BLAST, PSIBLAST and PHIBLAST, FASTA.
Gene finding : Using Genscan, HMMGene etc.
Protein structure : Tools for protein structure prediction.
Prediction
Annotation : Functional annotation.
Writing utilities using Perl.
TOTAL: 60 PERIODS
REFERENCES
1. Gusfield, Dan. Algorithms on strings Trees and Sequences, Cambridge University
Press.
2. Baldi, P., Brunak, S. Bioinformatics: The Machine Learning Approach, 2nd ed., East
West Press, 2003
3. Mount D.W. Bioinformatics: Sequence and Genome Analysis, Cold Spring Harbor
Laboratory Press, 2001.
4. Baxevanis A.D. and Oullette, B.F.F. A Practical Guide to the Analysis of Genes and
Proteins, 2nd ed., John Wiley, 2002
5. Tisdall, James, Beginning PERL for Bioinformatics, O’Reilley, 2001.6. Durbin, R. et
al., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic
Acids. Cambridge University Press, 1998.
BT 9212 COMPUTATIONAL BIOLOGY L T P C
2 0 2 3
UNIT I INTRODUCTION TO COMPUTATIONAL BIOLOGY 7
Molecular sequences. Sequence analysis. Dynamic programming. Pairwise and multiple
sequence alignment and motifs. Applications.
UNIT II DATABASES 6
Scoring matrices, heuristic methods of database searching: BLAST family of programs,
FASTA. Phylogenetic trees.
UNIT III INTRODUCTION TO GENOMICS AND PROTEOMICS 10
Functional, structural and comparative genomics. Gene finding and annotation. Protein
structure. Homology modeling. Differential gene expression.
UNIT IV MACHINE LEARNING TECHNIQUES 12
Hidden Markov models, Neural nets, Decision trees and their application in
computational biology. Eukaryotic and prokaryotic gene finding. DNA Computing.
UNIT V INTRODUCTION TO PERL 10
Variables, Data types, control flow constructs, arrays, lists and hashes, String
manipulation, File handling.
LAB:
Sequence analysis : Pairwise and multiple sequence alignment. Tools available
for sequence analysis. Motif generation.
Databases : Exploring biological databases
Database searching : Using BLAST, PSIBLAST and PHIBLAST, FASTA.
Gene finding : Using Genscan, HMMGene etc.
Protein structure : Tools for protein structure prediction.
Prediction
Annotation : Functional annotation.
Writing utilities using Perl.
TOTAL: 60 PERIODS
REFERENCES
1. Gusfield, Dan. Algorithms on strings Trees and Sequences, Cambridge University
Press.
2. Baldi, P., Brunak, S. Bioinformatics: The Machine Learning Approach, 2nd ed., East
West Press, 2003
3. Mount D.W. Bioinformatics: Sequence and Genome Analysis, Cold Spring Harbor
Laboratory Press, 2001.
4. Baxevanis A.D. and Oullette, B.F.F. A Practical Guide to the Analysis of Genes and
Proteins, 2nd ed., John Wiley, 2002
5. Tisdall, James, Beginning PERL for Bioinformatics, O’Reilley, 2001.6. Durbin, R. et
al., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic
Acids. Cambridge University Press, 1998.
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