BIOINFORMATICS & BIOLOGICAL DATABASES:
Introduction to Bioinformatics, Goals, Scope, Applications in biological science and medicine and Limitations,a) Sequence Databases b) Structure Databases c) Special Databases and applications: Genome, Microarray, Metabolic pathway, motif, multiple sequence alignment and domain databases. Mapping databases – genome wide maps. Chromosome specific human maps. Applications of these databases. Database Similarity Searching: Unique Requirements of Database Searching. Heuristic Databasesearching, Basic Local Alignment Search Tool (BLAST), FASTA, Comparison of FASTA and BLAST, Database Searching with the Smith– Waterman Method.
SEQUENCE ALIGNMENT:
Evolutionary basis, Homology vs Similarity, Similarity vs Identity. Types of Sequence alignment - Pairwise and Multiple sequence alignment, Alignment algorithms, Scoring matrices, Statistical significance of sequence alignment. Multiple Sequence Alignment: Scoring function, Exhaustive algorithms, Heuristic algorithms, Practical issues. Profiles and Hidden Markov Models: Position-Specific scoring matrices, Profiles, Markov Model and Hidden Markov Model.
PREDICTION MOTIFS AND DOMAINS:
Motif and Domain databases, Identification of Motifs and Domains in Multiple Sequence Alignment using Regular expressions, Motif and Domain Databases statistical models, Protein Family databases, Motif Discovery in unaligned sequences. Sequence logos. Gene and Promoter Prediction: Promoter and Regulatory elements in Prokaryotes and Eukaryotes. Promoter and Regulatory element prediction – algorithms. Gene prediction. Gene prediction in Prokaryotes and Eukaryotes. Categories of Gene Prediction Programs. Prediction algorithms. Discussions with case studies
PREDICTIVE METHODS:
Predictive methods using Nucleic acid sequence – DNA framework, Masking of repetitive DNA, predicting RNA secondary structure, Finding RNA genes, Detection offunctional sites and Codon bias in the DNA. Predictive methods using protein sequence – Protein identity and Physical properties. Structure prediction - Prediction of secondary structure of protein, Antigenic sites, Active sites, Folding classes, specialized structures and Tertiary structures. Discussions with case studies. Concepts involved in insilico Primer Designing and developing Restriction Maps
MOLECULAR PHYLOGENETICS:
Phylogenetics Basics. Molecular Evolution and Molecular Phylogenetics - Terminology, Gene Phylogeny vs Species Phylogeny, Forms of Tree Representation. Phylogenetic Tree Construction Methods and Programs - Distance-Based Methods, CharacterBased Methods. Phylogenetic Tree evaluation methods. Phylogenetic analysis software and algorithms. Bootstrap methods.