BINC SYLLABUS for all Papers BINC BioInformatics Syllabus - Basic

Major Bioinformatics Resources NCBI! "BI! "#PASy! 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 $pen access biblio%rap&ic resources an' literature 'atabases Open access bibliographic resources related to Life Sciences viz., ub!ed, "io!ed #entral, ublic Library of Sciences $ LoS% Se(uence 'atabases &ormats, 'uerying and retrieval (ucleic acid se'uence databases: )en"ank, *!"L, ++",rotein se'uence databases: .niprot/0": S12SS/ 3OT, Tr*!"L, 23/ S+ 3epositories for high throughput genomic se'uences: *ST, STS )SS, etc.)enome +atabases at (#"2, *"2, T2)3, S4()*3 5iral )enomes 4rcheal and "acterial )enomes*ukaryotic genomes with special reference to model organisms $6east, +rosophila, #. elegans, 3at, !ouse, 7uman, plants such as 4rabidopsis thaliana, 3ice, etc.% )* Structure *atabase +", (+" #hemical Structure database: ubchem )ene *8pression database: )*O, S4)* *eri+e' *atabases 0nowledge 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 se'uences and interpretation of the same Se'uence: 2nter ro, rosite, fam, ro+om, )ene Ontology Structure classification database: #4T7,S#O , &SS rotein/ rotein interaction database: ST32() Compilation of resources (43 +atabase and 1eb server 2ssues and other resources published in "ioinformatics related 9ournals

Se(uence Analysis
,ile formats 5arious file formats for bio/molecular se'uences: )en"ank, &4ST4, )#), !S& etc Basic concepts: Se'uence similarity, identity and homology, definitions of homologues, orthologues, paralogues :

Scorin% matrices basic concept of a scoring matri8, !atrices for nucleic acid and proteins se'uences, 4! and "LOS.! series, principles based on which these matrices are derived Pair-ise se(uence ali%nments basic concepts of se'uence alignment: local and global alignments, (eedleman and 1unsch, Smith and 1aterman algorithms for pairwise alignments, gap penalties, use of pairwise alignments for analysis of (ucleic acid and protein se'uences and interpretation of results Multiple se(uence ali%nments .MSA/ the need for !S4, basic concepts of various approaches for !S4 $e.g. progressive, hierarchical etc.%. 4lgorithm of #L.ST4L1 and ile.p and their application for se'uence analysis $including interpretation of results%, concept of dandrogram and its interpretation *atabase Searc&es 0eyword/based searches using tools like *(T3*; and S3S Se'uence/based searches: "L4ST and &4ST4 Se(uence patterns an' profiles "asic concept and definition of se'uence patterns, motifs and profiles, various types of pattern representations viz. consensus, regular e8pression $ rosite/type% and se'uence profiles- profile/based database searches using S2/"L4ST, analysis and interpretation of profile/based searches 0a#onomy an' p&ylo%eny "asic concepts in systematics, ta8onomy and phylogeny- molecular evolution- nature of data used in Ta8onomy and hylogeny, +efinition and description of phylogenetic trees and various types of trees Protein an' nucleic aci' properties #omputation of various parameters using proteomics tools at the *8 4Sy server and *!"OSS Comparati+e %enomics "asic concepts and applications, whole genome alignments: understanding significance. 4rtemis as an e8ample Structural Biolo%y )-* structure +isuali1ation an' simulation 5isualization of structures using 3asmol or S +"5 or #72!* or 5!+ "asic concepts in molecular modeling: different types of computer representations of molecules. *8ternal coordinates and 2nternal #oordinates (on/#ovalent 2nteractions and their role in "iomolecular structure and function &undamentals of 3eceptor/ligand interactions. Proteins rinciples of protein structure- eptide bond, phi, psi and chi torsion angles, ramachandran map, anatomy of proteins < 7ierarchical organization of protein structure < rimary. Secondary, Super secondary, Tertiary and =uaternary structure- 7ydrophobicity of amino acids, acking of protein structure, Structures of oligomeric proteins and study of interaction interfaces *NA an' RNA types of base pairing < 1atson/#rick and 7oogsteen- types of double helices $4, ", ;%, triple and 'uadruple stranded +(4 structures, geometrical as well as structural features- structural and geometrical parameters of each form and their comparison- various types of interactions of +(4 with proteins, small molecules 3(4 secondary and tertiary structures, t/3(4 tertiary structure Carbo&y'rates 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 )lyco/con9ugates: various types of glycolipids and glycoproteins Classification an' comparison of protein )* structures urpose of ?/+ structure comparison and concepts, 4lgorithms : #*, 54ST and +4L2, concept of coordinate transformation, 3!S+, ;/score for structural comparision +atabases of structure/based classification- #4T7, S#O and &SS Secon'ary structure pre'iction 4lgorithms viz. #hou &asman, )O3 methods- nearest neighbor and machine learning based methods, analysis of results and measuring the accuracy of predictions. 0ertiary Structure pre'iction &undamentals of the methods for ?+ structure prediction $se'uence similarity@identity of target proteins of known structure, fundamental principles of protein folding etc.% 7omology@comparative !odeling, fold recognition, threading approaches, and ab initio structure prediction methods

BINC BioInformatics Syllabus - A'+ance'

Se(uence analysis Scorin% matrices +etailed method of derivation of the 4! and "LOS.! matrices Pair-ise se(uence ali%nments (eedleman and 1uncsh, Smith and 1aterman algorithms and their implementation Multiple se(uence ali%nments .MSA/ Use of 2MM-base' Al%orit&m for !S4 $e.g. S4! method% Se(uence patterns an' profiles Repeats 0an'em an' Intersperse' repeats! repeat fin'in%! Motifs! consensus! position -ei%&t matrices 4lgorithms for derivation of and searching se'uence patterns: !*!*, 72/"L4ST, S#an rosite and 34TT 4lgorithms for generation of se'uence profiles: rofile 4nalysis method of )ribskov, 7!!er, S2/ "L4ST Protein an' nucleic aci' properties e.g. roteomics tools at the *8 4Sy server and *!"OSS 0a#onomy an' p&ylo%eny hylogenetic analysis algorithms such as ma8imum arsimony, . )!4, Transformed +istance, (eighbors/3elation, (eighbor/,oining, robabilistic models and associated algorithms such as robabilistic models of evolution and ma8imum likelihood algorithm, "ootstrapping methods, use of tools such as hylip, !ega, 4. 4nalysis of regulatory 3(4As: +atabases and tools Structural Biolo%y *8perimental methods for "iomolecular structure determination:B/ray and (!3 2dentification@assignment of secondary structural elements from the knowledge of ?/+ structure of macromolecule using +SS and ST32+* methods rediction of secondary structure: 7+ and S2/ 3*+ methods 0ertiary Structure pre'iction &undamentals of the methods for ?+ structure prediction $se'uence similarity@identity of target proteins of known structure, fundamental principles of protein folding etc.% 7omology !odeling, fold recognition, threading approaches, and ab/initio structure prediction methods Structure analysis an' +ali'ation dbsum, 1hatcheck, rocheck,5erify?+ and rosa22 #ritical assesment of Structure prediction$#4S % Structures of oligomeric proteins and study of interaction interfaces Molecular mo'elin% an' simulations !acro/molecular force fields, salvation, long/range forces )eometry optimization algorithms: Steepest descent, con9ugate gradient 5arious simulation techni'ues: !olecular mechanics, conformational searches, !olecular +ynamics, C

!onte #arlo, genetic algorithm approaches, 3igid and Semi/&le8ible !olecular +ocking 3enomics Large scale genome se'uencing strategies )enome assembly and annotation )enome databases of lants, animals and pathogens !etagenomics )ene networks: basic concepts, computational model such as Lambda receptor and lac operon rediction of genes, promoters, splice sites, regulatory regions: basic principles, application of methods to prokaryotic and eukaryotic genomes and interpretation of results "asic concepts on identification of disease genes, role of bioinformatics/O!2! database, reference genome se'uence, integrated genomic maps, gene e8pression profiling- identification of S( s, S( database $+bS( %. 3ole of S( in harmacogenomics, S( arrays +(4 microarray: database and basic tools, )ene *8pression Omnibus $)*O%, 4rray*8press, S4)* databases +(4 microarray: understanding of microarray data, normalizing microarray data, detecting differential gene e8pression, correlation of gene e8pression data to biological process and computational analysis tools $especially clustering approaches% Comparati+e %enomics "asic concepts and applications, "L4ST>, !ega"last algorithms, ip!aker, 452+, 5ista, !.!mer, applications of suffi8 tree in comparative genomics, synteny and gene order comparisons #omparative genomics databases: #lusters of Orthologous )roups $#O)s% ,unctional %enomics 4pplication of se'uence based and structure/based approaches to assignment of gene functions < e.g. se'uence comparison, structure analysis $especially active sites, binding sites% and comparison, pattern identification, etc. .se of various derived databases in function assignment, use of S( s for identification of genetic traits )ene@ rotein function prediction using !achine learning tools: supervised@unsupervised learning, (eural network, S5! etc Proteomics rotein arrays: basic principles #omputational methods for identification of polypeptides from mass spectrometry rotein arrays: bioinformatics/based tools for analysis of proteomics data $Tools available at *8 4Sy roteomics server%- databases $such as 2nter ro% and analysis tools rotein/protein interactions: databases such as ST32()S, +2 , protein/protein interactions !odeling biological systems Systems biology < .se of computers in simulation of cellular subsystems !etabolic networks, or network of metabolites and enzymes, Signal transduction networks, )ene D 2 server and tools for analysis of

regulatory networks, !etabolic pathways: databases such as 0*)), *! , !eta#yc, 4ra#yc *ru% 'esi%n +rug discovery process 3ole of "ioinformatics in drug design Target identification and validation and lead optimization +ifferent systems for representing chemical structure of small molecules like S!2L*S etc )eneration of ?+ coordinates of small molecules Structure/based drug design: 2dentification and 4nalysis of "inding sites and virtual screening Ligand based drug design: Structure 4ctivity 3elationship < =S43s and =S 3s, =S43 !ethodology, harmacophore mapping In silico prediction 4+!*T properties for +rug !olecules 4accine 'esi%n 3everse vaccinology and immunoinformatics +atabases in 2mmunology rinciples of "/cell and T/cell epitope prediction

Su%%este' Boo5s for Rea'in%

+avid 1 !ount! "ioinformatics: Se'uence 4nd )enome 4nalysis, >nd *dition, cold Spring 7arbor ress +urbin et al $>EEF% "iological Se'uence 4nalysis: robabilistic models of protein and (ucleic acids #ambridge .niversity ress. Thomas *. #reighton, roteins: structures and molecular properties #hemoinformatics *dited by ,ohann )asteiger and Thomas *ngel Structural "ioinformatics, *dited hilip *. "ourne and 7elge 1eissig

BINC Biolo%y Syllabus

Cell Biolo%y an' 3enetics

Basic

"asic aspects of rokaryotic and eukaryotic cells $plant and animal cells%- membranes and cellular compartments, cell organelles, structure and function #ell motility and shape: cytoskeletal elements, cilia and flagella- motor proteins #ell/cell interactions: 2ntercellular 9unctions #ell cycle and its regulation, events during mitosis and meiosis #oncepts of "ioenergetics, respiration, electron transport systems. #oncepts of gene: 4llele, multiple alleles, pseudoallele, complementation tests. !endelian principles : 2nheritance, se8 linked inheritance, +ominance, segregation, independent assortment. !utations : Types, causes and detection, !utant types < lethal, conditional, biochemical, loss of function, gain of function, germinal versus somatic mutants, point@deletion@insertional mutations. "asic concepts in immunology, antigen/antibody interaction, humoral and cell mediated immunity. #oncepts of development and pattern formation. Molecular Biolo%y rokaryotic genome organization and structure rokaryotic gene e8pression, factors involved in gene regulation *ukaryotic genome organization and structure, mechanisms of gene e8pression in *ukaryotes, basic mechanisms of transcription and translation !echanisms of genome alterations: 3ecombination, mutation, inversion, duplication, transposition. "asic concepts of replication. Bioc&emistry #arbohydrates and lipids, their importance in cells roteins: 4mino acids and their physico/chemical properties, peptide bond and peptides (ucleic acids: (ucleosides, nucleotides, 3(4 and +(4. +enaturation and renaturation of +(4 *nzymes: .nits of activity, coenzymes and metal cofactors, temperature and p7 effects, !ichaelis/ !enten kinetics, inhibitors and activators, active site #arbohydrate metabolism: )lycolysis, gluconeogenesis, glycogenolysis, glycogenesis, T#4 cycle and o8idative phosphorylation entose phosphate pathway- hormonal control, H/o8idation and biosynthesis of fatty acids Transamination and deamination of amino acids, ketogenic and glycogenic amino acids, urea cycle urine and pyrimidine biosynthesis F

BINC Biolo%y Syllabus 6 A'+ance'

Cell Biolo%y an' 3enetics 5esicular transport and protein traffic in cells +ifferent mechanisms of signal transduction, concepts in signal network, second messenger, molecules involved in various signaling pathways such as )/protein coupled receptors, protein kinases, calcium binding proteins *8tensions of !endelian principles : #odominance, incomplete dominance, gene interactions, pleiotropy, genomic imprinting, penetrance and e8pressivity, linkage and crossing over, se8 linkage, )ene mapping methods : Linkage maps, tetrad analysis, mapping with molecular markers, mapping by using somatic cell hybrids, development of mapping population in plants. *8tra chromosomal inheritance : 2nheritance of mitochondrial and chloroplast genes, maternal inheritance. "asic microbial genetics : !ethods of genetic transfers < transformation, con9ugation, transduction and se8duction, mapping genes by interrupted mating, fine structure analysis of genes. "asic 7uman genetics : edigree analysis, linkage testing, karyotypes, genetic disorders. opulation genetics, 7ardy 1einberg rinciple Molecular Biolo%y )enome organization, initiation, elongation and termination of transcription, template and enzyme properties, promoter and regulatory se'uences. 3egulation of translation, ost transcriptional modifications, processing of 3(4 and proteins !ethods for studying gene e8pression and regulatory se'uences, large/scale e8pression analysis, use of microarrays )enetic 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, #3, northern. Southern, western blotting, 3&L , fingerprinting, 34 +s, +(4 and protein se'uencing methods *pigenetic mechanisms of inheritance, regulatory 3(4 molecules $mi3(4, si3(4%, antisense 3(4 and their applications Bioc&emistry *nzyme kinetics, Lineweaver/"urk plot, competitive and non competitive inhibition !olecular mechanisms of interactions of small and large molecules including ions, regulation of protein pathways, mechanism of enzyme action and ribozymes 2soenzymes, allosteric enzymes, regulation by covalent modification !echanism of enzyme action with special reference to lysozyme and carbo8ypeptidase < 4. &unctional classification of enzymes, concept of *# numbers. Organization of metabolic systems: *nzyme chains, multi enzyme comple8es and multifunctional enzymes and regulatory enzymes.. I

2nborn errors of metabolism. #oncept of biochemical regulation, feed back and feed forward systems, biochemical oscillations

Su%%este' Boo5s for Rea'in%

:. ?. rinciples of "iochemistry by Lehninger )enes B by ". Lewin >. The !olecular biology of the #ell by 4lberts et al C. *ssential #ell "iology >nd *d ".4lberts, +."ray, 0.7opkin and 4.,ohnson D. "iochemisty, Gth *dition "erg, ,ermy !., Tymoczko, ,ohn L and Styer, Lubert G. "iochemistry 5ol:: "iomolecules, mechanisms of enzyme action and metabolism 5oet, + and 5oet, ,. F. !olecular "iology of the )ene, 1atson, ,+., 7opkins,(7., 3oberts, ,1 and Steitz,,4

BINC P&ysical Science syllabus Basic

article dynamics, (ewtonAs laws of motion, velocity, acceleration, momentum. #onservative forces, #onservation of *nergy. &irst law of thermodynamics, second law of thermodynamics, reversible and irreversible processes, 2sothermal, isobaric and 'uasistatic processes. #oncepts of *nthalpy and *ntropy, 2nterrelation between potential energy and force. Thermodynamic, )ibbs and 7elmholtz free energies. #hemical potential. &irst/order phase transitions *'uation of state for ideal gases. +epartures from ideality. !a8well/"oltzman +istribution

BINC P&ysical Science Syllabus -A'+ance'

*lectrostatics, #oulombKs Law, +ielectric #onstant, dipole/dipole and dipole/monopole interaction "asic roperties of lasers. =uantum mechanics: the time/independent SchrLdinger e'uation, energy eigenvalues and eigenfunctions. Simple solvable models in =uantum !echanics: article in a bo8, harmonic oscillator, hydrogen like atoms.

Su%%este' Boo5s for Rea'in%

1. &undamentals of hysics, Gth *dition +avid 7alliday M 3obert 3esnik >. The &eynman Lectures on hysics: 5olumes :, > M ?

BINC C&emical Science Syllabus

Basic

7ybridization states of atoms. *lectronic structure of molecules, #hemical bonding $ionic bonds, covalent bonds, hydrogen bond, hydrophobic effects, coordinate bonds%. "asic !olecular orbital theory. 5alence bonds. (on/covalent bonding in protein structure. Tautomerization, geometrical isomerism, inductive effect, stereochemsitry $3@S,+@L%- nucleophile, electrophile, nucleophilic substitution, electrophilic substitution, nomenclature of organic compounds. "ioisosterism. &irst law of thermodynamics, isothermal process, entropy and second law of thermodynamics, reversible and irreversible processes- #oncepts of enthalpy, internal energy and potential energy- 2nter/ relation between potential energy and force, heat of formation. #oncept of p7, p0, chemical e'uilibrium, 7enderson/7asselbach e'uation, structure of water.

BINC C&emical Science Syllabus A'+ance'

#oncept of free energy, activation energy. olar molecules, molar refraction and polarization. "asic !olecular orbital theory. +ipole moment, potentiometric determination of p0 of aminoacids. "iophysical techni'ues for determining size and shape of macromolecules < ultra centrifugation, electrophoresis and chromatography. 4pplication of spectroscopy and B/ray diffraction for determination of biomolecular secondary and tertiary structure. !ass/spectroscopy of biological molecules. Luminescence, fluorescence, phosphorescence. &irst law of thermodynamics, isothermal process, entropy and second law of thermodynamics, reversible and irreversible processes- #oncepts and calculations of enthalpy, internal energy and potential energy, free energy, entropy- 2nter/relation between potential energy and force, heat of formation. "asic principles of chemical kinetics < ;ero, first and second order kinetics, enzyme kinetics: !ichaelis /!enten kinetics- 4ctivation energy and the 4rrhenius law.

Su%%este' Boo5s for Rea'in%

hysical #hemistry, .1.4tkins and and ,ulio de aula Organic #hemistry , !orrison M "oyd. "iophysical chemistry vol 2 ,#harles 3 #antor M aul 3einhard Schimmel

BINC Mathematics and Statistics Syllabus Basic

Mathematics Functions and Graphs of polynomial, logarithm, exponential and trigonometric functions. 2D co-ordinate 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: Chi-square, t and F distributions. Central limit theorem. Methods of least squares and regression analysis. Estimation: un-biased, maximum likelihood. Testing of hypothesis: Type I and Type II errors, power of a test, p-value. 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.

Su%%este' Boo5s for Rea'in%

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 Iinformation 0ec&nolo%y Syllabus Basic

&undamentals in #omputing Types of rocessing: "atch, 3eal/Time, Online, Offline. Types of modern computing: 1orkstations, Servers, arallel rocessing #omputing, #luster computing, )rid computing 2ntroduction to operating systems: Operating System concept, .(2B@L2(.B. "asic rogramming #oncepts < se'uential, conditional and loop constructs 2ntroduction to +atabase Systems S=L =ueries )eometric transformation #oordinate transformations

BINC Information 0ec&nolo%y Syllabus A'+ance'

4. +ata Structures and 4lgorithm 4rrays, Link Lists, Stacks, =ueues, )raphs, Trees < rograms to be implemented using eith # or ,ava Sorting, Searching, string comparison < programs using erl ". +atabases S=L, inde8ing and 7ashing.

Su%%este' Boo5s for Rea'in%

:. >. ?. C. 5. +atabase !anagement System < 3amakrishnan and )ehrke +ata Structure : 4ndrew S Tannenbaum #omplete 3eference to # #omplete 3eference to ,ava Complete Reference to Perl