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BIOINFORMATICS

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BIOINFORMATICS

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jajokox546
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54.

BIOINFORMATICS
Unit 1: Concepts in Computing
Fundamentals of Computing, Introduction to Operating Systems, WINDOWS, UNIX/Linux
operating systems, Batch Processing, Multi-programmed Batch System, Time Sharing
System, Distributed System, Real Time System, Dead lock, CPU scheduling, Computer
Security, Visualization techniques, Viewing in three dimension, Image Processing with
emphasis on biological systems, Computer Networking, Security of the network, Network
topology and architecture, Hierarchical networks, TCP/IP family of protocols, Parallel &
High performance computing, Cloud computing

Unit 2: Programming Languages


Programming in C, Variables and operators, Control Flow statements and loops, Arrays and
Pointers, string, Functions, File handling in C, Overview of Object Oriented Programming
using Python: class and objects, functions and operator overloading, inheritance, Introduction
to PERL, BioPerl modules, Web technology using PHP and Python.

Unit 3: Database Management System and Biological Databases


Definition, purpose, advantage, components of Database System; Data Models; Three level
Architecture for Database System –internal, conceptual and external levels; Role of
Schemas, Client/Server architecture; Relational Databases: Relational data models (binary,
ternary, quaternary & n-ary relations), Primary and secondary keys, Data Definition
Language; Data Manipulation Language; Structured Query Language; Classification of
biological databases; Nucleic acid, protein, genome and structural databases; tools and
databases for sequence submission and retrieval; Concepts of Bigdata and NoSQL.

Unit 4: Mathematics and Statistics


Coordinate geometry: Basic concepts of 2D and 3D geometry; Vector algebra– Addition and
subtraction of vectors, Dot and cross product; Matrix algebra: basic definitions, matrix
operations, transpose of a matrix, inverse of matrix, Eigen values, Eigen vectors; Introduction
to Probability and Statistics, Conditional probability, Bayes’ theorem; Random variable,
mathematical expectation; Frequency distributions, Descriptive Statistics; Probability
Distributions: Binomial, Multinomial, Poisson and Normal Distribution; Introduction and
properties of ‘t’, Chi-square and F distributions; Hypothesis testing; Basic concepts of
Simple Random sampling and Stratified random sampling; Correlation and regression;
Cluster Analysis-Hierarchical and Non-Hierarchical methods, Principal Component Analysis;
Hidden Markov Models.

Unit 5: Biochemistry, Molecular Biology and Biotechnology


Biochemistry: Hydrophobic, electrostatic and van der Waals forces, General introduction to
physical techniques for determination of structure of biopolymers, Structure, properties and
functions of amino acids, proteins, and nucleic acids, Anatomy of Proteins - Secondary
structures, Motifs, Domains, Tertiary and quaternary structures, Classification of Protein
topologies, Helices and sheets, Helix-coil theory, Conformation of polypeptides and side
chains, molten globules, enzymes and folding pathways; Molecular Biology and
Biotechnology: Nucleic acids as genetic material, Genetic code, Genome organization and
regulation in prokaryotes and eukaryotes, DNA replication, transcription and translation,
recombinant DNA technology, Site directed mutagenesis, Mutation, RNA editing, RNA
processing;

Unit 6: Genomics and Proteomics


Genomics: Classical ways of genome analysis, Evolution of sequencing technologies,
Genomic libraries, Physical mapping of genomes; Genome sequencing strategies: Sequencing
by synthesis, ligation, single molecular sequencing; Microarrays analysis and applications;

pg. 140
Next generation sequencing technologies, Sequence assembly and annotation, exome
sequencing; Genome structural and functional annotation; Functional genomics; Candidate
gene identification, Linkage analysis, genotyping analysis; Whole genome analysis and
comparative genomics; ncRNAs; Genome Editing; Proteomics: Mass spectrometry and
analysis, peptide identification and protein interface; Metabolomics for elucidating metabolic
pathways; Applications of genomics and proteomics in agriculture;

Unit 7: Analytical Bioinformatics


Introduction, origin, history of Bioinformatics; Bioinformatics applications in agriculture;
Basic concepts of sequence similarity, Sequences alignments: local and global alignment,
pairwise and multiple sequence alignment, Dynamic programming-Needleman and Wunsch,
Smith-Waterman algorithms; Scoring matrices: PAM & BLOSUM, Motifs and Patterns;
Analysis of nucleotide and protein sequences: Pre-processing of NGS data, Bowtie, BWA,
HISAT, FM Index, Assembly assessment measures, Quantification of gene expression:
RPKM, FPKM, TPM; ncRNA analysis; Phylogenetic analyses: Types of phylogenetic trees,
Tree-Building Methods: Character-based and Distance-based methods; Tree Evaluation:
Bootstrapping; Introduction to systems and network biology; Tools and models for GWAS
and Genomic Selection; Data mining & Knowledge discovery, Machine learning techniques:
Supervised and unsupervised learning, Artificial Neural Network, Support Vector Machine,
Random Forest; Deep Learning;

Unit 8: Molecular Modelling and drug designing


Concepts of Protein Modelling, Molecular mechanics, Force Fields, Local and global energy
minima, Energy minimization techniques; Algorithms in predicting secondary structure of
proteins- Chau-Fasman algorithm, Protein folding energy landscape; Protein structure
prediction: ab initio, homology modeling and fold recognition methods, Ramachandran plot;
Visualization tools: Rasmol, SwissPDB, PyMol, QMol; Techniques of MD Simulation,
Simulated annealing; RNA Secondary Structure prediction techniques, Algorithmic
perspective of RNA folding; Drug designing: Receptor-based and ligand-based drug design,
Design of ligands, docking, Classical SAR/QSAR, Molecular descriptors, Pharmacophore
mapping and applications.

Unit 9: Data structures and Algorithms


Linear and non-linear data structure: Linked list, Stack, Queues, Trees-Terminologies, Binary
trees, Tree traversal (Pre-order, In-order, post-order), AVL trees, Graph theory, Depth-first
search and Breadth-first search algorithms; Algorithms and complexity, Iterative and
recursive algorithms, Big-O Notation, Algorithm design and analysis techniques, Greedy
Algorithms, Randomized Algorithms, Divide-and-Conquer approach, Searching and Sorting
algorithms;

pg. 141

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