Bioinformatics BT SEM III

Bioinformatics SEM III Biotechnology

Course Objective: The objective of this course is to familiarize students with basic concepts of

sequences, structural alignment, database searching, protein structure prediction.

Detail Contents

UNIT-1

Introduction to Bioinformatics Resources

Bioinformatics Resources: NCBI, EBI, ExPASy, RCSB, DDBJ: The knowledge of databases and bioinformatics tools available at these resources, organization of databases: data contents, purpose and utility. Open access bibliographic resources and literature databases: PubMed, BioMed Central, Public Library of Sciences (PloS), Cite Xplore.

UNIT-2

Sequence databases

Sequence databases: Nucleic acid sequence databases: GenBank, EMBL, DDBJ; Protein sequence databases: Uniprot-KB: SWISS-PROT, TrEMBL, UniParc; Structure Databases: PDB, NDB, PubChem, ChemBank. Sequence file formats: Various file formats for bio-molecular sequences:

GenBank, FASTA, GCG, MSF etc. Protein and nucleic acid properties: Proteomics tools at the ExPASy server, GCG utilities and EMBOSS, Computation of various parameters

UNIT-3

Sequence analysis

Sequence Analysis: Basic concepts of sequence similarity, identity and homology, definitions of homologues, orthologues, paralogues and xenologues Scoring matrices: basic concept of a scoring matrix, Matrices for nucleic acid and proteins sequences, PAM and BLOSUM series, matrix derivation methods and principles.

UNIT-4

Sequence alignment

Sequence alignment: Measurement of sequence similarity; Similarity and homology. Pairwise sequence alignment: Basic concepts of sequence alignment, 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.      

BTL-E-202 Lab Course:

• • 1  Proteomics tools,

  • 2  Structural and functional predictions,

  • 3  Phylogenetic Analysis, Phylogenetic tree construction

  • 4  DNA and protein sequence and PDB file formats,

  • 5  Local and global sequence alignment of protein and DNA sequences,

  • 6  Needleman Wunsch and Smith-Waterman algorithm,

  • 7  BLAST, Multiple sequence alignment,

Reference

• 1. Bioinformatics: Sequence and Genome Analysis by Mount D., Cold Spring Harbor Laboratory Press, New York. 2004

  2. Bioinformatics- a Practical Guide to the Analysis of Genes and Proteins by Baxevanis, A.D.and Francis Ouellellette, B.F., Wiley India Pvt Ltd. 2009

  3. Introduction to bioinformatics by Teresa K. Attwood, David J. Parry-Smith, Pearson Education. 1999

  4. Bioinformatics for Dummies by Jean-michel Claverie Cedric Notredame. Publisher: Dummies (Jan 2007)