BINC SYLLABUS for Paper-II BINC BioInformatics Syllabus - Advanced

Sequence analysis Scorin matrices! Detailed method of derivation of the PAM and BLOSUM matrices Pair"ise sequence ali nments! Needleman and Wuncsh, Smith and Waterman algorithms and their implementation #ultiple sequence ali nments $#SA%! Use of &##-based Al orit'm for MSA e!g! SAM method" Sequence patterns and profiles! (epeats! )andem and Interspersed repeats* repeat findin * #otifs* consensus* position "ei 't matrices Algorithms for derivation of and searching se#uence patterns$ M%M%, P&'(BLAS), S*anProsite and P+A)) Algorithms for generation of se#uence profiles$ Profile Anal,sis method of -ri.s/ov, &MMer, PS'( BLAS) Protein and nucleic acid properties! e!g! Proteomics tools at the %0PAS, server and %MBOSS )a+onomy and p'ylo eny! Ph,logenetic anal,sis algorithms such as ma0imum Parsimon,, UP-MA, )ransformed Distance, Neigh.ors(+elation, Neigh.or(1oining, Pro.a.ilistic models and associated algorithms such as Pro.a.ilistic models of evolution and ma0imum li/elihood algorithm, Bootstrapping methods, use of tools such as Ph,lip, Mega, PAUP Anal,sis of regulator, +NA2s$ Data.ases and tools Structural Biolo y %0perimental methods for Biomolecular structure determination$3(ra, and NM+ 'dentification4assignment of secondar, structural elements from the /no5ledge of 6(D structure of macromolecule using DSSP and S)+'D% methods Prediction of secondar, structure$ P&D and PS'(P+%D methods )ertiary Structure prediction! 7undamentals of the methods for 6D structure prediction se#uence similarit,4identit, of target proteins of /no5n structure, fundamental principles of protein folding etc!" &omolog, Modeling, fold recognition, threading approaches, and a.(initio structure prediction methods Structure analysis and validation! Pd.sum, Whatchec/, Prochec/,8erif,6D and Prosa'' *ritical assesment of Structure prediction *ASP" Structures of oligomeric proteins and stud, of interaction interfaces #olecular modelin and simulations Macro(molecular force fields, salvation, long(range forces -eometr, optimi9ation algorithms$ Steepest descent, con:ugate gradient 8arious simulation techni#ues$ Molecular mechanics, conformational searches, Molecular D,namics, ;

Monte *arlo, genetic algorithm approaches, +igid and Semi(7le0i.le Molecular Doc/ing ,enomics Large scale genome se#uencing strategies -enome assem.l, and annotation -enome data.ases of Plants, animals and pathogens Metagenomics -ene net5or/s$ .asic concepts, computational model such as Lam.da receptor and lac operon Prediction of genes, promoters, splice sites, regulator, regions$ .asic principles, application of methods to pro/ar,otic and eu/ar,otic genomes and interpretation of results Basic concepts on identification of disease genes, role of .ioinformatics(OM'M data.ase, reference genome se#uence, integrated genomic maps, gene e0pression profiling< identification of SNPs, SNP data.ase D.SNP"! +ole of SNP in Pharmacogenomics, SNP arra,s DNA microarra,$ data.ase and .asic tools, -ene %0pression Omni.us -%O", Arra,%0press, SA-% data.ases DNA microarra,$ understanding of microarra, data, normali9ing microarra, data, detecting differential gene e0pression, correlation of gene e0pression data to .iological process and computational anal,sis tools especiall, clustering approaches" Comparative enomics! Basic concepts and applications, BLAS)=, MegaBlast algorithms, PipMa/er, A8'D, 8ista, MUMmer, applications of suffi0 tree in comparative genomics, s,nten, and gene order comparisons *omparative genomics data.ases$ *lusters of Orthologous -roups *O-s" -unctional enomics! Application of se#uence .ased and structure(.ased approaches to assignment of gene functions > e!g! se#uence comparison, structure anal,sis especiall, active sites, .inding sites" and comparison, pattern identification, etc! Use of various derived data.ases in function assignment, use of SNPs for identification of genetic traits -ene4Protein function prediction using Machine learning tools$ supervised4unsupervised learning, Neural net5or/, S8M etc Proteomics Protein arra,s$ .asic principles *omputational methods for identification of pol,peptides from mass spectrometr, Protein arra,s$ .ioinformatics(.ased tools for anal,sis of proteomics data )ools availa.le at %0PAS, Proteomics server"< data.ases such as 'nterPro" and anal,sis tools Protein(protein interactions$ data.ases such as S)+'N-S, D'P, PP' server and tools for anal,sis of protein(protein interactions Modeling .iological s,stems S,stems .iolog, > Use of computers in simulation of cellular su.s,stems Meta.olic net5or/s, or net5or/ of meta.olites and en9,mes, Signal transduction net5or/s, -ene =

regulator, net5or/s, Meta.olic path5a,s$ data.ases such as ?%--, %MP , Meta*,c, Ara*,c .ru desi n Drug discover, process +ole of Bioinformatics in drug design )arget identification and validation and lead optimi9ation Different s,stems for representing chemical structure of small molecules li/e SM'L%S etc -eneration of 6D coordinates of small molecules Structure(.ased drug design$ 'dentification and Anal,sis of Binding sites and virtual screening Ligand .ased drug design$ Structure Activit, +elationship > @SA+s and @SP+s, @SA+ Methodolog,, Pharmacophore mapping In silico prediction ADM%) properties for Drug Molecules /accine desi n! +everse vaccinolog, and immunoinformatics Data.ases in 'mmunolog, Principles of B(cell and )(cell epitope prediction

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David W Mount* Bioinformatics$ Se#uence And -enome Anal,sis, =nd %dition, cold Spring &ar.or Press Dur.in et al =AAB" Biological Se#uence Anal,sis$ Pro.a.ilistic models of protein and Nucleic acids *am.ridge Universit, Press! )homas %! *reighton, Proteins$ structures and molecular properties *hemoinformatics %dited ., 1ohann -asteiger and )homas %ngel Structural Bioinformatics, %dited Philip %! Bourne and &elge Weissig

BINC Biolo y Syllabus 1 Advanced

Cell Biolo y and ,enetics 8esicular transport and protein traffic in cells Different mechanisms of signal transduction, concepts in signal net5or/, second messenger, molecules involved in various signaling path5a,s such as -(protein coupled receptors, protein /inases, calcium .inding proteins %0tensions of Mendelian principles $ *odominance, incomplete dominance, gene interactions, pleiotrop,, genomic imprinting, penetrance and e0pressivit,, lin/age and crossing over, se0 lin/age, -ene mapping methods $ Lin/age maps, tetrad anal,sis, mapping 5ith molecular mar/ers, mapping ., using somatic cell h,.rids, development of mapping population in plants! %0tra chromosomal inheritance $ 'nheritance of mitochondrial and chloroplast genes, maternal inheritance! 6

Basic micro.ial genetics $ Methods of genetic transfers > transformation, con:ugation, transduction and se0duction, mapping genes ., interrupted mating, fine structure anal,sis of genes! Basic &uman genetics $ Pedigree anal,sis, lin/age testing, /ar,ot,pes, genetic disorders! Population genetics, &ard, Wein.erg Principle #olecular Biolo y -enome organi9ation, initiation, elongation and termination of transcription, template and en9,me properties, promoter and regulator, se#uences! +egulation of translation, Post transcriptional modifications, processing of +NA and proteins Methods for stud,ing gene e0pression and regulator, se#uences, large(scale e0pression anal,sis, use of microarra,s -enetic information transfer, details of regulation in eu/ar,otes and pro/ar,otes, hori9ontal gene transfer Organi9ation of eu/ar,otic genomes, methods for stud,ing variation and pol,morphism at genome level, P*+, northern! Southern, 5estern .lotting, +7LP, fingerprinting, +APDs, DNA and protein se#uencing methods %pigenetic mechanisms of inheritance, regulator, +NA molecules mi+NA, si+NA", antisense +NA and their applications Bioc'emistry %n9,me /inetics, Line5eaver(Bur/ plot, competitive and non competitive inhi.ition Molecular mechanisms of interactions of small and large molecules including ions, regulation of protein path5a,s, mechanism of en9,me action and ri.o9,mes 'soen9,mes, allosteric en9,mes, regulation ., covalent modification Mechanism of en9,me action 5ith special reference to l,so9,me and car.o0,peptidase > A! 7unctional classification of en9,mes, concept of %* num.ers! Organi9ation of meta.olic s,stems$ %n9,me chains, multi en9,me comple0es and multifunctional en9,mes and regulator, en9,mes!! 'n.orn errors of meta.olism! *oncept of .iochemical regulation, feed .ac/ and feed for5ard s,stems, .iochemical oscillations

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;! Principles of Biochemistr, ., Lehninger =! )he Molecular .iolog, of the *ell ., Al.erts et al 6! -enes 3 ., B! Le5in C! %ssential *ell Biolog, =nd %d B!Al.erts, D!Bra,, ?!&op/in and A!1ohnson D! Biochemist,, Eth %dition Berg, 1erm, M!, ),moc9/o, 1ohn L and St,er, Lu.ert E! Biochemistr, 8ol;$ Biomolecules, mechanisms of en9,me action and meta.olism 8oet, D and 8oet, 1! B! Molecular Biolog, of the -ene, Watson, 1D!, &op/ins,N&!, +o.erts, 1W and Steit9,1A C

BINC P'ysical Science Syllabus -Advanced

%lectrostatics, *oulom.Fs La5, Dielectric *onstant, dipole(dipole and dipole(monopole interaction Basic Properties of lasers! @uantum mechanics$ the time(independent SchrGdinger e#uation, energ, eigenvalues and eigenfunctions! Simple solva.le models in @uantum Mechanics$ Particle in a .o0, harmonic oscillator, h,drogen li/e atoms!

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1. 7undamentals of Ph,sics, Eth %dition David &allida, H +o.ert +esni/ =! )he 7e,nman Lectures on Ph,sics$ 8olumes ;, = H 6

BINC C'emical Science Syllabus ! Advanced

*oncept of free energ,, activation energ,! Polar molecules, molar refraction and polari9ation! Basic Molecular or.ital theor,! Dipole moment, potentiometric determination of p? of aminoacids! Bioph,sical techni#ues for determining si9e and shape of macromolecules > ultra centrifugation, electrophoresis and chromatograph,! Application of spectroscop, and 3(ra, diffraction for determination of .iomolecular secondar, and tertiar, structure! Mass(spectroscop, of .iological molecules! Luminescence, fluorescence, phosphorescence! 7irst la5 of thermod,namics, isothermal process, entrop, and second la5 of thermod,namics, reversi.le and irreversi.le processes< *oncepts and calculations of enthalp,, internal energ, and potential energ,, free energ,, entrop,< 'nter(relation .et5een potential energ, and force, heat of formation! Basic principles of chemical /inetics > Iero, first and second order /inetics, en9,me /inetics$ Michaelis (Menten /inetics< Activation energ, and the Arrhenius la5!

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Ph,sical *hemistr,, P!W!At/ins and and 1ulio de Paula Organic *hemistr, , Morrison H Bo,d! Bioph,sical chemistr, vol ' ,*harles + *antor H Paul +einhard Schimmel

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.

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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 )ec'nolo y Syllabus !Advanced

A! Data Structures and Algorithm Arra,s, Lin/ Lists, Stac/s, @ueues, -raphs, )rees > Programs to .e implemented using eith * or 1ava Sorting, Searching, string comparison > programs using Perl B! Data.ases S@L, inde0ing and &ashing!

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Data.ase Management S,stem > +ama/rishnan and -ehr/e Data Structure $ Andre5 S )annen.aum *omplete +eference to * *omplete +eference to 1ava Complete Reference to Perl