Introduction to Bioinformatics

Contents: 1. Essentials of computer: i. Introduction to bioinformatics. ii. Applications of bioinformatics. iii. Networking. iv. Introduction to SQL. 2. Bioprogramming: i. C++. ii. Bio Perl. iii. Biojava. 3. Softwares and applications: i. Clustal. W. ii. Ras Mol. iii. Molscript. iv. Tree view. v. Alscript. vi. Phylip. 4. Databases: i. What is a database? ii. Different types of biological databases. iii. Database similarity searches. iv. Sqlj and Sqi *plus. v. Internet based biological databases. vi. Sequence databases. vii. Data mining and visualisation. 5. Sequence alignments: i. Dot plots. ii. Needleman-Wunsch. iii. Smith-waterman. iv. Similarity matrices and Penalties. v. Multiple sequence alignments-scoring, mathematical optimal and heuristic methods. 6. Sequence searches in biological databases: i. BLAST 1 and BLAST 2. ii. FASTA. iii. PHI and PSI BLAST. iv. Phylogenetic trees-distance based phylogenies-UPGMA and neighbour joining. v. Character based phylogenies-parsimony trees and maximum likelihood method. 7. Genomics and genome analysis: i. Data analysis. ii. Gene prediction (prokaryotic, eukaryotic, promoter prediction, transcription factor binding sites). iii. Protein function prediction. iv. Genome comparison and pattern matching. v. Substitution patterns. 8. Proteomics and proteome: i. Visualisation and modeling with secondary structure prediction. ii. Localization/hydrophobicity and analysis of domains. iii. 3D alignment and folding classes, with families and domains. iv. DNA chips. v. Normalisation of data/statistical evaluation. 9. Drug designing: i. Stabilisation and substrate specificity. ii. Rationale for drug design. iii. Humanisation of antibodies. v. Protein/protein docking and protein/ligand docking.