Course

Introduction to Bioinformatics – applications of Bioinformatics – challenges and opportunities – introduction to NCBI data model- Various file formats for biological sequences.

Bioinformatics resources – Importance of databases – Biological databases- Primary & Secondary databases (Genbank, EMBL, DDBJ, Swiss Prot , PDB, NDB, BLOCKS, Pfam, ProSITE, etc.).

Sequence alignment methods: Sequence analysis of biological data-Significance of sequence alignment- pairwise sequence alignment methods- Use of scoring matrices and gap penalties in sequence alignments- PAM and BLOSUM Scoring Matrices. Introduction to Dynamic Programming, Global alignments: Needleman Wunsch Algorithm, Local Alignments: Smith Waterman Algorithm, Gap Penalties. Multiple sequence alignment methods – Tools and application of multiple sequence alignment. Sequence alignment tools (BLAST, FASTA, CLUSTAL-W/X, MUSCLE, TCOFFEE), Variants of BLAST (BLASTn, BLASTp, PSIBLAST, PHI-BLA

Phylogenetic analysis algorithms: Maximum Parsimony, UPGMA, Transformed Distance, Neighbors-Relation, Neighbor-Joining, jackknife, Probabilistic models and associated algorithms such as Probabilistic models of evolution and maximum likelihood algorithm, Bootstrapping methods, use of tools such as PHYLIP, MEGA, PAUP.

1. 1 Higgins,Des and Taylor Williw: Bioinformatics: Sequence , Structure and databanks, Oxford , University Press,2000.
2. Baxenvants, , Bioinformatics: A practical guide to the analysis of genes and proteins”, Third edition, John wiley & Sons ,2005
3. Teresa Attwood, Introduction To Bioinformatics ,Pearson Education Singapore Pte Ltd, 2007
4. Mount, DW, Bioinformatics: Sequence and Genome analysis”, Second edition, Cold Spring Harbor
5. Laboratory Baxevanis 5. A.D., Davison D.B., Page R. D. M. & Petsko G.A. Current Protocols in Bioinformatics. New York, John Wiley & Sons Inc., 2004. ISBN: 0555015254
6. 6 S.C. Rastogi et al, Bioinformatics: Methods and Applications: (Genomics, Proteomics and Drug Discovery) Kindle Edition.