Bioinformatics National Certification BINC Examination 2015
BINC 2015 Exam Date : : BINC 2015 Application Form
Department of Biotechnology,
Government of India, New Delhi & Pondicherry University,
Website : www.btisnet.nic.in/binc.asp
BINC 2015 Exam Date
|BINC 2015 Exam Date for Part I ( Paper – I ) : 07th June, 2015; 10:00 A.M. – 12:00 P.M.
BINC 2015 Exam Date for Part II ( Paper II – & Paper III ) : 28th June, 2015; 9:00 AM to 12:00 PM – 2:00 PM – 4:00 P.M.
BINC 2015 Syllabus
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 Library of Sciences ( PLoS )
Formats, querying and retrieval
Nucleic acid sequence databases : GenBank, EMBL, DDBJ;
Protein sequence databases : Uniprot – KB : SWISS – PROT, TrEMBL, PIR – PSD
Repositories for high throughput genomic sequences: EST, STS GSS, etc.;
Genome Databases at NCBI, EBI, TIGR, SANGER
Archeal and Bacterial Genomes;
Eukaryotic genomes with special reference to model organisms ( Yeast, Drosophila, C. elegans, Rat, Mouse, Human, plants such as Arabidopsis thaliana, Rice, etc. )
3D Structure Database: PDB, NDB
Chemical Structure database : Pubchem
Gene Expression database : GEO, SAGE
Knowledge of the following databases with respect to: basic concept of derived databases, sources of primary data and basic principles of the method for deriving the secondary data, organization of data, contents and formats of database entries, identification of patterns in given sequences and interpretation of the same
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
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
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, Needleman and Wunsch, Smith and Waterman algorithms for pairwise alignments, gap penalties, use of pairwise alignments for analysis of Nucleic acid and protein sequences and interpretation of results
Multiple sequence alignments ( MSA ) : the need for MSA, basic concepts of various approaches for MSA ( e.g. progressive, hierarchical etc. ). Algorithm of CLUSTALW and PileUp and their application for sequence analysis (including interpretation of results ), concept of dandrogram and its interpretation
Database Searches :
Keyword – based searches using tools like ENTREZ and SRS
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
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.
External coordinates and Internal Coordinates
Non – Covalent Interactions and their role in Biomolecular structure and function
Fundamentals of Receptor – ligand interactions.
Proteins : Principles of protein structure; Peptide bond, phi, psi and chi torsion angles, ramachandran map, anatomy of proteins – Hierarchical organization of protein structure – Primary. Secondary, Super 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
Classification and comparison of protein 3D structures :
Purpose of 3 – D structure comparison and concepts, Algorithms : CE, VAST and DALI, concept of coordinate transformation, RMSD, Z – score for structural comparision Databases of structure – based classification; CATH, SCOP and FSSP
Secondary structure prediction : Algorithms viz. Chou Fasman, GOR methods; nearest neighbor and machine learning based methods, analysis of results and measuring the accuracy of predictions.
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
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
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, Monte Carlo, genetic algorithm approaches, Rigid and Semi – Flexible Molecular Docking
Large scale genome sequencing strategies
Genome assembly and annotation
Genome databases of Plants, animals and pathogens
Gene networks : basic concepts, computational model such as Lambda receptor and lac operon
Prediction of genes, promoters, splice sites, regulatory regions : basic principles, application of methods to prokaryotic and eukaryotic genomes and interpretation of results
Basic concepts on identification of disease genes, role of bioinformatics – OMIM database, reference genome sequence, integrated genomic maps, gene expression profiling; identification of SNPs, SNP database ( DbSNP ). Role of SNP in Pharmacogenomics, SNP arrays
DNA microarray : database and basic tools, Gene Expression Omnibus (GEO), ArrayExpress, SAGE databases
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
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 regulatory networks, Metabolic pathways : databases such as KEGG, EMP , MetaCyc, AraCyc
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
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.
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.
Carbohydrates and lipids, their importance in cells
Proteins : Amino acids and their physico-chemical properties, peptide bond and peptides
Nucleic acids : Nucleosides, nucleotides, RNA and DNA. Denaturation and renaturation of DNA
Enzymes : Units of activity, coenzymes and metal cofactors, temperature and pH effects, MichaelisMenten kinetics, inhibitors and activators, active site
Carbohydrate metabolism : Glycolysis, gluconeogenesis, glycogenolysis, glycogenesis, TCA cycle and oxidative phosphorylation
Pentose phosphate pathway; hormonal control, β-oxidation and biosynthesis of fatty acids
Transamination and deamination of amino acids, ketogenic and glycogenic amino acids, urea cycle
Purine and pyrimidine biosynthesis
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
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 sequencing methods
Epigenetic mechanisms of inheritance, regulatory RNA molecules ( miRNA, siRNA ), antisense RNA and their applications
Enzyme kinetics, Lineweaver-Burk plot, competitive and non competitive inhibition
Molecular mechanisms of interactions of small and large molecules including ions, regulation of protein pathways, mechanism of enzyme action and ribozymes
Isoenzymes, allosteric enzymes, regulation by covalent modification
Mechanism of enzyme action with special reference to lysozyme and carboxypeptidase – A.
Functional classification of enzymes, concept of EC numbers.
Organization of metabolic systems : Enzyme chains, multi enzyme complexes and multifunctional enzymes and regulatory enzymes..
Inborn errors of metabolism. Concept of biochemical regulation, feed back and feed forward systems, biochemical oscillations
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.
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.
BINC Mathematics and Statistics Syllabus – Basic
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.
Differentiation and integration of the above mentioned functions.
Matrix algebra : Multiplication, inverse and solution of linear equations.
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
Vector – addition, subtraction, multiplication and their geometric understanding.
Matrices, their eigenvalues and eigenvectors.
Differential equations: Second order linear differential equation and initial value problems.
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.
BINC Iinformation 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
BINC Information Technology Syllabus : Advanced
A. Data Structures and Algorithm
Arrays, Link Lists, Stacks, Queues, Graphs, Trees – Programs to be implemented using C or Python or Java Sorting, Searching, string comparison – programs using Perl
SQL, indexing and Hashing.
BINC 2015 Exam Date – BINC 2015 Eligibility – BINC 2015 Exam Pattern – BINC 2015 Syllabus.
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