Bioinformatics I

Nucleotide databases, Protein databases, Specialized databases; Laboratory data submission and data retrieval; Various file formats for biomolecular sequences: Genbank, EMBL, FASTA, GCG, msf, nbrf-pir etc.; Basic concepts of sequence similarity: identity and homology, definitions of homologues, orthologues, paralogues; Sequence patterns and profiles

Introduction, Evolutionary Basis of Sequence Alignment, Optimal alignment method, Statistical Significance of Alignment. Database searching Artifacts; Database similarity searching: FASTA, BLAST, Various versions of basic BLAST and FASTA, Advance version of BLAST: PHI-BLAST and profile-based database searches using PSIBLAST; Multiple sequence alignment: progressive method and Iterative method; Applications of pairwise and multiple sequence alignment; Tools for multiple sequence alignment: CLUSTALW and Pileup (Algorithmic concepts).

Basic concept of a scoring matrix, Similarity and distance matrix, Substitution matrices: Matrices for nucleic acid and proteins sequences, PAM and BLOSUM series, Principles based on which these matrices are derived and Gap Penalty; Predictive Method using Nucleotide Sequence: Introduction, Marking repetitive DNA, Database search, Codon bias detection, detecting functional site in DNA.

Phylogeny and concepts in molecular evolution; nature of data used in taxonomy and phylogeny; definition and description of Phylogenetic trees and various types of trees; Different methods of Phylogenetic tree construction: UPGMA and Fitch-Margoliash Algorithm; case studies in phylogenetic sequence analysis.

Protein identification based on composition, Physical properties based on sequence, Motif and pattern, Secondary structure (Statistical method: Chou Fasman and GOR method, Neural Network and Nearest neighbor method) and folding classes, specialized structure or features, Tertiary structures (Homology Modeling); Structure visualization methods (RASMOL, CHIME etc.); Protein Structure alignment and analysis. Application of bioinformatics in drug discovery and drug designing. B.Tech. (Biotechnology) 3rd Year Dr. A.P.J. Abdul Kalam Technical University Uttar Pradesh, Lucknow