BT8651 - BIOINFORMATICS (Syllabus) 2017-regulation Anna University

BT8651 - BIOINFORMATICS (Syllabus) 2017-regulation Anna University

BT8651	BIOINFORMATICS	LPTC

3003

OBJECTIVES:

• To improve the programming skills of the student
• To let the students know the recent evolution in biological science

UNIT I	INTRODUCTION	(9+6)

Introduction to Operating systems, Linux commands, File transfer protocols ftp and telnet, Introduction to Bioinformatics and Computational Biology, Biological sequences, Biological databases, Genome specific databases, Data file formats, Data life cycle, Database management system models, Basics of Structured Query Language (SQL).

UNIT II	SEQUENCE ALIGNMENT	(9+6)

Sequence Analysis, Pair wise alignment, Dynamic programming algorithms for computing edit distance, string similarity, shotgun DNA sequencing, end space free alignment. Multiple sequence alignment, Algorithms for Multiple sequence alignment, Generating motifs and profiles, Local and Global alignment, Needleman and Wunsch algorithm, Smith Waterman algorithm, BLAST, PSIBLAST and PHIBLAST algorithms.

UNIT III	PHYLOGENETIC METHODS	(9+6)

Introduction to phylogenetics, Distance based trees UPGMA trees, Molecular clock theory, Ultrametric trees, Parsimonious trees, Neighbour joining trees, trees based on morphological traits, Bootstrapping. Protein Secondary structure and tertiary structure prediction methods, Homology modeling, abinitio approaches, Threading, Critical Assessment of Structure Prediction, Structural genomics.

UNIT IV	PROTEIN STRUCTURE ANALYSIS	(9+6)

Machine learning techniques: Artificial Neural Networks in protein secondary structure prediction, Hidden Markov Models for gene finding, Decision trees, Support Vector Machines. Introduction to Systems Biology and Synthetic Biology, Microarray analysis, DNA computing,Bioinformatics approaches for drug discovery, Applications of informatics techniques in genomics and proteomics: Assembling the genome, STS content mapping for clone contigs, Functional annotation, Peptide mass fingerprinting.

UNIT V	PERL PROGRAMMING	(9+6)

Basics of PERL programming for Bioinformatics: Data types: scalars and collections, operators, Program control flow constructs, Library Functions: String specific functions, User defined functions, File handling.

TOTAL : 75 PERIODS

OUTCOMES: Upon completion of this course, students will be able to

• Develop bioinformatics tools with programming skills.
• Apply computational based solutions for biological perspectives.
• Pursue higher education in this field.
• Practice life-long learning of applied biological science.

TEXT BOOKS:

1. Introduction to Bioinformatics by Arthur K. Lesk , Oxford University Press.
2. Algorithms on Strings, Trees and Sequences by Dan Gusfield, Cambridge University Press.
3. Biological Sequence Analysis Probabilistic Models of proteins and nucleic acids by R.Durbin, S.Eddy, A.Krogh, G.Mitchison.
4. Bioinformatics Sequence and Genome Analysis by David W. Mount, Cold Spring Harbor Laboratory Press.
5. Beginning Perl for Bioinformatics: An introduction to Perl for Biologists by James Tindall, O’Reilley Media

REFERENCE:

1. Bioinformatics The Machine Learning Approach by Pierre Baldi and Soren Brunak.