This is
Basic Bioinformatics Syllabus for Binc Paper 1 examination. Knowing each topic thoroughly is very task to do for preparing
BINC Paper 1 examination.
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
Bioinformatics 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 forMSA (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
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 andprofiles, 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, Phylogenetic tree and its reconstruction.
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
Structural Biology
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 comparison.
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
Suggested Books for Reading:
David W Mount, Bioinformatics: Sequence and Genome Analysis, 2nd Edition, cold Spring Harbor Press
Durbin et al (2007) Biological Sequence Analysis: Probabilistic models of protein and Nucleic acids Cambridge University Press.
Stuart M.Brown (2013) Next-generation DNA sequencing Informatics. Cold Spring Harbor Press
M.E.J. Newman (2010) Networks: An Introduction, Oxford University Press.
Thomas E. Creighton, Proteins: structures and molecular properties
Chemoinformatics Edited by Johann Gasteiger and Thomas Engel
Structural Bioinformatics, Edited Philip E. Bourne and Helge Weissig
Lee A Segel (2008), Biological Kinetics, Cambridge University Press, Cambridge
Cornish-Bowden (2012), Fundamentals of Enzyme Kinetics ,Wiley-Blackwell
Alberghina L (2005), System Biology : Definitions and Perspectives, Springer-Verlag Berlin Heidelberg.
Najarian K, Najarian S, Gharibzadeh S, Eichelberger CN (2009)
Systems Biology and Bioinformatics: A Computational Approach, CRC Press.
Klipp E, Liebermeister W, Wierling C, Kowald A, Lehrach H, Herwig R (2009) Systems Biology : A Text Book, Wiley-Blackwell
Integrative approaches for finding modular structure in biological
networks, NATURE REVIEWS , GENETICS, VOLUME 14, OCTOBER 2013
BIOINFORMATICS, Vol. 19 no. 2, 2003
Nucleic Acids Research (2014), Vol. 42, Database issue D199–D205 doi:10.1093/nar/gkt1076
Nucleic Acids Research (2012), Vol. 40, Database issue D109–D114 doi:10.1093/nar/gkr988
An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks (2011), Integrative Biology, 2011.3, 1071-1086.
Computational Systems Bioinformatics — Methods and Biomedical Applications By Xiaobo Zhou (Harvard Medical School and Brigham & Women's Hospital, USA), Stephen T C Wong (Harvard Medical School and Brigham & Women's Hospital, USA).
Bioinformatics for Systems Biology (2009) by Stephen Krawetz, Published by Humana Press.
