Organisation : Pondicherry University
Announcement : Syllabus
Name Of The Exam : Bio Informatics National Certification BINC Exam

Download Syllabus : http://www.indianjobtalks.com/uploads/75859-Binc.pdf
Home Page : http://www.pondiuni.edu.in/exams/binc/

BINC Exam Syllabus :
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)

Sequence databases : 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 Viral Genomes 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

Derived Databases : 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 Bio informatics 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
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 dendrogram and its interpretation

BINC BioInformatics Syllabus - Advanced
Sequence analysis :
Scoring matrices: Detailed method of derivation of the PAM and BLOSUM matrices
Pairwise sequence alignments: Needleman and Wunsch, 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, PSI-BLAST
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, Bayesian inference 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 Assessment 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

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
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.
Next Generation sequencing & assembly: Elements of big data analysis, NGS Platforms based on pyrosequencing, sequencing by synthesis, emulsion PCR approach with small magnetic beads and single molecule real time (SMRT) sequencing; Genome assembly algorithms, De-novo assembly algorithms, Sequence Alignment formats: Sequence Alignment/Map (SAM) format, Binary Alignment/Map (BAM) format.

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), Ensembl

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