Bioinformatics & Computer Application

Syllabus

Unit 1

Major Bioinformatics Resources: NCBI, EBI, ExPASy, RCSB; Open access bibliographic resources and literature databases: PubMed, BioMed Central; Sequence & Structural Database; Genomic resources; Data access, retrieval and submission; Data access standard search engines, Data retrieval tools: Entrez, DBGET & SRS

Unit II

Sequence Analysis: Introduction to sequence analysis; Local and global Alignment; Pairwise and Multiple string alignment, Sequence Alignment algorithms: Dot Matrix, Needleman & Wunsch algorithms, Smith-Waterman algorithm; Substitution Matixes (PAM, BLOSUM), BLAST, FASTA algorithms. Methods of phylogenetic analysis: Steps of phylogenetic analysis; Classification of phylogeny: graphs, trees and cladograms.

Unit III

Patterns, Motifs and profiles in sequences; Structure classification of proteins (SCOP, CATH); Protein Secondary structure prediction; Tertiary structure prediction methods; Protein structure prediction by comparative modeling approaches. Introduction to molecular modeling and Drug designing.

Reference Book

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Slides

Unit I

  1. Introduction
  2. GenBank & NCBI
  3. Uniprot & G. Browsers
  4. BioLiterature

Unit II

  1. Pairwise Sequence Alignment (Introduction)
  2. Gaps, PAM & BLOSUM
  3. Global & Local Alignment
  4. BLAST
  5. Multiple Sequence Alignment
  6. Molecular Evolution & Phylogeny (paper regarding Trees using MEGA)

Unit III

  1. Patterns, Motifs & Profiles
  2. SCOP & CATH
  3. Protein Structure Prediction
  4. Comparative Modeling
  5. Advanced Protein Structure Prediction
  6. Secondary Structure Prediction
  7. Drug Discovery

BCB Lab Manual

Bioinformatics and Functional Genomics 2nd Edition