Unit-I
Introduction to Bioinformatics
Scope of Bioinformatics, Elementary Commands and Protocols,ftp,telnet,http,Primer on information theory
Unit II
Special topics in Bioinformatics
DNA mapping and sequencing,map alignment.Large scale sequencing methods ,shortgun and sanger method,cDNA sequencing Genome mapping ,map assembly, Comparative sequence analysis.
Unit III
Sequencing Alignment and Dynamic Programming
Alignment-Local,Global alignment,pairwise and multiple sequence alignments.Concept of gap penalty and e-value.Alignment algorithms.Dynamic programming in sequence alignment:Needleman-Wunsch Algorithm and Smith Waterman Algorithm,Aminoacid Substitution matrices (PAM,BLOSUM).Sequence similarity search with database:BLAST and FASTA.
Unit IV
Primary database Information
Introduction to Biological databases,organization and management of databases,searching and retrieval of information from world wide web.Structure databases-PDB (protein data Bank),Molecular Modeling databases(MMDB),Primary databases NCBL,EMBL,DDBJ.
Unit V
Secondary database
Introduction to Biological databases,organization and management of databases Swissprot,PIR,KEGG
Unit VI
Phylogenetic analysis and tree building
Introduction to phylogenetics,Methods of phylogenetic analysis,role of multiple sequence alignment algorithms in phylogenetic analysis,Automated tools for phylogenetic analysis,Construction of phylogenetic tree.
UnitVII
Biochemical database
Introduction to Biological databases,organization and management of databases,KEGG,EXGESCY,BRENDA,ERGO
Unit VIII
Introduction to Homology
Introduction to Homology,Levels of protein structure,homology modeling of proteins (Sequence to structure) Cn3D,rasMol and SPDbv in homology modeling –case studies