BINC Basic Bioinformatics Syllabus=> Paper 1

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.

Share this

AEI Online Tutor