Subsections
[Cr:4, Lc:1, Tt:0, Lb:6]
- Biological databases: Nucleic acid and protein databases such as ENTREZ, Genbank. File formats of nucleotide and protein sequences such as FASTA, ASN.1, Genbank flatfile.
- DNA and protein sequence analysis: Data storage and compression, DNA sequence composition, primer design, Motif and pattern search methods, Sequence alignments (Pairwise and multiple sequence alignment), Local and global sequence alignments, Scoring matrices such as PAM and BLOSUM. Consensus pattern, motifs and Profiles. Position Specific Scoring Matrices.
- Methods for Database Searching BLAST and FASTA. Significance of alignments, E-values. BLAST programs: BLASTp, BLASTn, BLASTx, tBLASTn, tBLASTx, PSI BLAST.
- Phylogenetic analysis: Concept of phylogenetic trees-Branches, nodes, internal nodes, rooted and unrooted trees. Distance matrix methods; Maximum parsimony methods; Maximum likelihood methods.
- Gene prediction: Prokaryotes versus eukaryotes. Promoters,splice sites. RNA secondary structure prediction.
- Structural bioinformatics: Introduction to protein tertirary structure analysis, Protein structure visualization, Protein structure classification and databases. Ramachandran map, Protein secondary structure prediction. Tertiary structure prediction: Homology modeling, Threading/Fold recognition, ab initio protein structure prediction.
- 4 to 6 weeks project on sequence or/and structure analysis.
- J. Xiong, Essential Bioinformatics, Cambridge University Press (2009).
- D. Mount, Bioinformatics: Sequence and Genome Analysis, 2nd Edn., Cold Spring Harbor Laboratory Press (2004).
- A. D. Baxevanis and B. F. F. Ouellette (eds),Bioinformatics: A practical guide to the analysis of genes and proteins, 3rd Edn., Wiley-Interscience (2004).
- D. E. Krane and M. L. Raymer, Fundamental concepts of Bioinformatics, 1st Edn., Pearson Education India (2003).
