BINC SYLLABUS for Paper-III 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 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. D. +atabase !anagement System < 3amakrishnan and )ehrke +ata Structure : 4ndrew S Tannenbaum #omplete 3eference to # #omplete 3eference to ,ava #omplete 3eference to erl