| Re: Bio Informatics National Certification BINC Examination
Syllabus & Books:
The syllabus of that exam contains the following subjects:
Bioinformatics,
Biology,
Physical Science,
Chemical Science,
Mathematics & Statistics,
Information Technology
The detailed syllabus is as given below with the name of the books:
BINC SYLLABUS for all Papers:
BINC Bioinformatics Syllabus - Basic
Major Bioinformatics Resources: NCBI, EBI, ExPASy, RCSB
The knowledge of various databases and bioinformatics tools available at these resources, organization
of databases: data contents and formats, purpose and utility in Life Sciences
Open access bibliographic resources and literature databases:
Open access bibliographic resources related to Life Sciences viz., PubMed, BioMed Central, Public
Sequence: InterPro, Prosite, Pfam, ProDom, Gene Ontology
Structure classification database: CATH,SCOP, FSSP
Protein-Protein interaction database: STRING
Compilation of resources: NAR Database and Web server Issues and other resources published in
Bioinformatics related journals
Sequence Analysis
File formats:Various file formats for bio-molecular sequences: GenBank, FASTA, GCG, MSF etc
Basic concepts: Sequence similarity, identity and homology, definitions of homologues, orthologues,
paralogues
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Scoring matrices: basic concept of a scoring matrix, Matrices for nucleic acid and proteins sequences,
PAM and BLOSUM series, principles based on which these matrices are derived
Pairwise sequence alignments: basic concepts of sequence alignment: local and global alignments,
Sequence-based searches: BLAST and FASTA
Sequence patterns and profiles: Basic concept and definition of sequence patterns, motifs and
profiles, various types of pattern representations viz. consensus, regular expression (Prosite-type) and
sequence profiles; profile-based database searches using PSI-BLAST, analysis and interpretation of
profile-based searches
Taxonomy and phylogeny: Basic concepts in systematics, taxonomy and phylogeny; molecular
evolution; nature of data used in Taxonomy and Phylogeny, Definition and description of phylogenetic
trees and various types of trees
Protein and nucleic acid properties: Computation of various parameters using proteomics tools at the
ExPASy server and EMBOSS
Comparative genomics: Basic concepts and applications, whole genome alignments: understanding
significance. Artemis as an example
Structural Biology
3-D structure visualization and simulation: Visualization of structures using Rasmol or SPDBV or
CHIME or VMD
Basic concepts in molecular modeling: different types of computer representations of molecules.
secondary, Tertiary and Quaternary structure; Hydrophobicity of amino acids, Packing of protein
structure, Structures of oligomeric proteins and study of interaction interfaces
DNA and RNA: types of base pairing – Watson-Crick and Hoogsteen; types of double helices (A, B,
Z), triple and quadruple stranded DNA structures, geometrical as well as structural features; structural
and geometrical parameters of each form and their comparison; various types of interactions of DNA
with proteins, small molecules
RNA secondary and tertiary structures, t-RNA tertiary structure
Carbohydrates: The various building blocks (monosaccharides), configurations and conformations of the building blocks; formations of polysaccharides and structural diversity due to the different types of linkages
Glyco-conjugates: various types of glycolipids and glycoproteins
Tertiary Structure prediction: Fundamentals of the methods for 3D structure prediction (sequence
similarity/identity of target proteins of known structure, fundamental principles of protein folding etc.)
Homology/comparative Modeling, fold recognition, threading approaches, and ab initio structure
prediction methods
BINC BioInformatics Syllabus - Advanced
Sequence analysis
Scoring matrices: Detailed method of derivation of the PAM and BLOSUM matrices
Pairwise sequence alignments: Needleman and Wuncsh, Smith and Waterman algorithms and their
implementation
Multiple sequence alignments (MSA):
Use of HMM-based Algorithm for MSA (e.g. SAM method)
Sequence patterns and profiles:
Repeats: Tandem and Interspersed repeats, repeat finding, Motifs, consensus, position weight
matrices
Algorithms for derivation of and searching sequence patterns: MEME, PHI-BLAST, SCanProsite and
PRATT
Algorithms for generation of sequence profiles: Profile Analysis method of Gribskov, HMMer, PSIBLAST
Protein and nucleic acid properties: e.g. Proteomics tools at the ExPASy server and EMBOSS
Taxonomy and phylogeny: Phylogenetic analysis algorithms such as maximum Parsimony, UPGMA,
Transformed Distance, Neighbors-Relation, Neighbor-Joining, Probabilistic models and associated
algorithms such as Probabilistic models of evolution and maximum likelihood algorithm,
Bootstrapping methods, use of tools such as Phylip, Mega, PAUP
Analysis of regulatory RNA’s: Databases and tools
Structural Biology
Experimental methods for Biomolecular structure determination:X-ray and NMR
Identification/assignment of secondary structural elements from the knowledge of 3-D structure of
macromolecule using DSSP and STRIDE methods
Prediction of secondary structure: PHD and PSI-PRED methods
Tertiary Structure prediction: Fundamentals of the methods for 3D structure prediction (sequence
similarity/identity of target proteins of known structure, fundamental principles of protein folding etc.)
Homology Modeling, fold recognition, threading approaches, and ab-initio structure prediction
methods
Structure analysis and validation: Pdbsum, Whatcheck, Procheck,Verify3D and ProsaII
Critical assesment of Structure prediction(CASP)
Structures of oligomeric proteins and study of interaction interfaces
Molecular modeling and simulations
Macro-molecular force fields, salvation, long-range forces
Geometry optimization algorithms: Steepest descent, conjugate gradient
Various simulation techniques: Molecular mechanics, conformational searches, Molecular Dynamics,
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Monte Carlo, genetic algorithm approaches, Rigid and Semi-Flexible Molecular Docking
Genomics
Large scale genome sequencing strategies
Genome assembly and annotation
Genome databases of Plants, animals and pathogens
Metagenomics
Gene networks: basic concepts, computational model such as Lambda receptor and lac operon
DNA microarray: understanding of microarray data, normalizing microarray data, detecting differential
gene expression, correlation of gene expression data to biological process and computational analysis
tools (especially clustering approaches)
Comparative genomics:
Basic concepts and applications, BLAST2, MegaBlast algorithms, PipMaker, AVID, Vista, MUMmer,
applications of suffix tree in comparative genomics, synteny and gene order comparisons
Comparative genomics databases: Clusters of Orthologous Groups (COGs)
Functional genomics:
Application of sequence based and structure-based approaches to assignment of gene functions – e.g.
sequence comparison, structure analysis (especially active sites, binding sites) and comparison, pattern
identification, etc. Use of various derived databases in function assignment, use of SNPs for
identification of genetic traits
Gene/Protein function prediction using Machine learning tools: supervised/unsupervised learning,
Neural network, SVM etc
Proteomics
Protein arrays: basic principles
Computational methods for identification of polypeptides from mass spectrometry
Protein arrays: bioinformatics-based tools for analysis of proteomics data (Tools available at ExPASy
Proteomics server); databases (such as InterPro) and analysis tools
Protein-protein interactions: databases such as STRINGS, DIP, PPI server and tools for analysis of
protein-protein interactions
Modeling biological systems
Systems biology – Use of computers in simulation of cellular subsystems
Metabolic networks, or network of metabolites and enzymes, Signal transduction networks, Gene
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regulatory networks, Metabolic pathways: databases such as KEGG, EMP , MetaCyc, AraCyc
Drug design
Drug discovery process
Role of Bioinformatics in drug design
Target identification and validation and lead optimization
Different systems for representing chemical structure of small molecules like SMILES etc
Generation of 3D coordinates of small molecules
Structure-based drug design: Identification and Analysis of Binding sites and virtual screening
Ligand based drug design: Structure Activity Relationship – QSARs and QSPRs, QSAR Methodology,
Pharmacophore mapping
In silico prediction ADMET properties for Drug Molecules
Vaccine design:
Reverse vaccinology and immunoinformatics
Databases in Immunology
Principles of B-cell and T-cell epitope prediction
Suggested Books for Reading:
David W Mount, Bioinformatics: Sequence And Genome Analysis, 2nd Edition, cold Spring Harbor
Press
Durbin et al (2007) Biological Sequence Analysis: Probabilistic models of protein and Nucleic acids
Cambridge University Press
Thomas E. Creighton, Proteins: structures and molecular properties
Chemoinformatics Edited by Johann Gasteiger and Thomas Engel
Structural Bioinformatics, Edited Philip E. Bourne and Helge Weissig
BINC Biology Syllabus: Basic
Cell Biology and Genetics
Basic aspects of Prokaryotic and eukaryotic cells (plant and animal cells); membranes and cellular
compartments, cell organelles, structure and function
Cell motility and shape: cytoskeletal elements, cilia and flagella; motor proteins
Cell-cell interactions: Intercellular junctions
Cell cycle and its regulation, events during mitosis and meiosis
Concepts of Bioenergetics, respiration, electron transport systems.
Concepts of gene: Allele, multiple alleles, pseudoallele, complementation tests.
Mendelian principles : Inheritance, sex linked inheritance, Dominance, segregation, independent
assortment.
Mutations : Types, causes and detection, Mutant types – lethal, conditional, biochemical, loss of
function, gain of function, germinal versus somatic mutants, point/deletion/insertional mutations.
Basic concepts in immunology, antigen-antibody interaction, humoral and cell mediated immunity.
Concepts of development and pattern formation.
Molecular Biology
Prokaryotic genome organization and structure
Prokaryotic gene expression, factors involved in gene regulation
Eukaryotic genome organization and structure, mechanisms of gene expression in Eukaryotes, basic
mechanisms of transcription and translation
Mechanisms of genome alterations: Recombination, mutation, inversion, duplication, transposition.
Basic concepts of replication
BINC Biology Syllabus – Advanced
Cell Biology and Genetics
Vesicular transport and protein traffic in cells
Different mechanisms of signal transduction, concepts in signal network, second messenger, molecules
involved in various signaling pathways such as G-protein coupled receptors, protein kinases, calcium
binding proteins
Extensions of Mendelian principles : Codominance, incomplete dominance, gene interactions,
pleiotropy, genomic imprinting, penetrance and expressivity, linkage and crossing over, sex linkage,
Gene mapping methods : Linkage maps, tetrad analysis, mapping with molecular markers, mapping
by using somatic cell hybrids, development of mapping population in plants.
Extra chromosomal inheritance : Inheritance of mitochondrial and chloroplast genes, maternal
inheritance.
Basic microbial genetics : Methods of genetic transfers – transformation, conjugation, transduction and
sexduction, mapping genes by interrupted mating, fine structure analysis of genes.
Basic Human genetics : Pedigree analysis, linkage testing, karyotypes, genetic disorders.
Population genetics, Hardy Weinberg Principle
Molecular Biology
Genome organization, initiation, elongation and termination of transcription, template and enzyme
properties, promoter and regulatory sequences. Regulation of translation, Post transcriptional
modifications, processing of RNA and proteins
Methods for studying gene expression and regulatory sequences, large-scale expression analysis, use of
microarrays
Genetic information transfer, details of regulation in eukaryotes and prokaryotes, horizontal gene
transfer
Organization of eukaryotic genomes, methods for studying variation and polymorphism at genome
level, PCR, northern. Southern, western blotting, RFLP, fingerprinting, RAPDs, DNA and protein
Inborn errors of metabolism Concept of biochemical regulation, feed back and feed forward systems, biochemical oscillations
Suggested Books for Reading:
1. Principles of Biochemistry by Lehninger
2. The Molecular biology of the Cell by Alberts et al
3. Genes X by B. Lewin
4. Essential Cell Biology 2nd Ed B.Alberts, D.Bray, K.Hopkin and A.Johnson
5. Biochemisty, 6th Edition Berg, Jermy M., Tymoczko, John L and Styer, Lubert
6. Biochemistry Vol1: Biomolecules, mechanisms of enzyme action and metabolism Voet, D and
Voet, J.
7. Molecular Biology of the Gene, Watson, JD., Hopkins,NH., Roberts, JW and Steitz,JA
BINC Physical Science syllabus : Basic
Particle dynamics, Newton’s laws of motion, velocity, acceleration, momentum Conservative forces,
Conservation of Energy
First law of thermodynamics, second law of thermodynamics, reversible and irreversible processes,
Isothermal, isobaric and quasistatic processes Concepts of Enthalpy and Entropy, Interrelation between potential energy and force Thermodynamic, Gibbs and Helmholtz free energies. Chemical potential. First-order phase transitions Equation of state for ideal gases. Departures from ideality Maxwell-Boltzman Distribution
BINC Physical Science Syllabus -Advanced
Electrostatics, Coulomb's Law, Dielectric Constant, dipole-dipole and dipole-monopole interaction
Basic Properties of lasers.
Quantum mechanics: the time-independent Schrödinger equation, energy eigenvalues and
eigenfunctions. Simple solvable models in Quantum Mechanics: Particle in a box, harmonic oscillator,
hydrogen like atoms.
Suggested Books for Reading:
1. Fundamentals of Physics, 6th Edition David Halliday & Robert Resnik
2. The Feynman Lectures on Physics: Volumes 1, 2 & 3
BINC Chemical Science Syllabus : Basic
Hybridization states of atoms. Electronic structure of molecules, Chemical bonding (ionic bonds,
covalent bonds, hydrogen bond, hydrophobic effects, coordinate bonds). Basic Molecular orbital
theory. Valence bonds Non-covalent bonding in protein structure
Tautomerization, geometrical isomerism, inductive effect, stereochemsitry (R/S,D/L); nucleophile,
electrophile, nucleophilic substitution, electrophilic substitution, nomenclature of organic compounds.
Bioisosterism.
First law of thermodynamics, isothermal process, entropy and second law of thermodynamics,
reversible and irreversible processes; Concepts of enthalpy, internal energy and potential energy; Interrelation
between potential energy and force, heat of formation.
Concept of pH, pK, chemical equilibrium, Henderson-Hasselbach equation, structure of water
BINC Chemical Science Syllabus: Advanced
Concept of free energy, activation energy Polar molecules, molar refraction and polarization Basic
Molecular orbital theory Dipole moment, potentiometric determination of pK of aminoacids
Biophysical techniques for determining size and shape of macromolecules – ultra centrifugation,
electrophoresis and chromatography. Application of spectroscopy and X-ray diffraction for
determination of biomolecular secondary and tertiary structure. Mass-spectroscopy of biological molecules Luminescence, fluorescence, phosphorescence
First law of thermodynamics, isothermal process, entropy and second law of thermodynamics, reversible and irreversible processes; Concepts and calculations of enthalpy, internal energy and potential energy, free energy, entropy; Inter-relation between potential energy and force, heat of formation.
Basic principles of chemical kinetics – Zero, first and second order kinetics, enzyme kinetics:
Michaelis -Menten kinetics; Activation energy and the Arrhenius law.
Suggested Books for Reading:
Physical Chemistry, P.W.Atkins and and Julio de Paula
Organic Chemistry, Morrison & Boyd
Biophysical chemistry vol I, Charles R Cantor & Paul Reinhard Schimmel
BINC Mathematics and Statistics Syllabus – Basic
Mathematics
Functions and Graphs of polynomial, logarithm, exponential and trigonometric functions
2D coordinate geometry: Equation of a line, circle, ellipse, parabola, hyperbola; focal
point, eccentricity and other properties.
3D geometry: Equation of sphere.
Solution of simultaneous and quadratic equations Sequences and series Limits.
Differentiation and integration of the above mentioned functions.
Matrix algebra: Multiplication, inverse and solution of linear equations.
Statistics
Discrete random variables, their probability mass function, probability distribution function, mean and variance.
Binomial and Poisson random variables and their properties
Continuous random variable, their probability density function, probability distribution
function, mean and variance.
Normal random variable and its properties
Conditional probability and Bayes’ theorem
BINC Mathematics, Statistics Syllabus – Advanced
Mathematics
Vector – addition, subtraction, multiplication and their geometric understanding.
Matrices, their eigenvalues and eigenvectors
Differential equations: Second order linear differential equation and initial value
problems.
Statistics
Sampling distributions: Chisquare,
t and F distributions.
Central limit theorem
Methods of least squares and regression analysis
Estimation: unbiased,
maximum likelihood.
Testing of hypothesis: Type I and Type II errors, power of a test, pvalue.
Large sample test: one and two sample tests for mean and variance.
Confidence interval for unknown mean and variance
Markov chains, their transition probability and stationary distributions.
Suggested Books for Reading:
Hogg, Mckean and Craig: Introduction to Mathematical Statistics, 6th Edition, Pearson
Prentice Hall, 2005
Sheldon M. Ross: Introduction to probability models, 9th Edition, Academic Press, 2007
Gilbert Strang: Linear Algebra and its application, 4th Edition, Cengage Learning, 2006
NCERT class 12 mathematics books
Ewens and Grant: Statistical methods in bioinformatics
BINC Information Technology Syllabus : Basic
Fundamentals in Computing
Types of Processing: Batch, Real-Time, Online, Offline.
Types of modern computing: Workstations, Servers, Parallel Processing Computing, Cluster
computing, Grid computing
Introduction to operating systems: Operating System concept, UNIX/LINUX.
Basic Programming Concepts – sequential, conditional and loop constructs
Introduction to Database Systems
SQL Queries
Geometric transformation
Coordinate transformations
BINC Information Technology Syllabus: Advanced
A. Data Structures and Algorithm
Arrays, Link Lists, Stacks, Queues, Graphs, Trees – Programs to be implemented using eith C
or Java
Sorting, Searching, string comparison – programs using Perl
B. Databases
SQL, indexing and Hashing
Suggested Books for Reading:
1. Database Management System – Ramakrishnan and Gehrke
2. Data Structure: Andrew S Tannenbaum
3. Complete Reference to C
4. Complete Reference to Java
5. Complete Reference to Perl
for the complete syllabus download the PDF file attached with it
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