Subsections
[Cr:4, Lc:1, Tt:0, Lb:9]
- Biological databases. Nucleic acid and protein databases.ENTREZ.
Genbank. Nucleotide and protein sequence data formats: FASTA, ASN.1,
Genbank Flatfile
- Pairwise and Multiple alignment. Homology, Sequence Identity and
Sequence similarity. Global alignment, Local alignment, Scoring
functions. Gap penalty. Statistical significance. PAM and BLOSUM.
Applications of Multiple sequence alignments: Consensus, motifs and
Profiles. Position Specific Scoring Matrices. Clustal X.
- Methods for Database Searching BLAST and FASTA. Scoring matrices,
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. Protein secondary structure prediction.
Tertiary structure prediction: Homology modeling, Threading , Fold
recognition, ab initio protein structure prediction. Protein structure
visualization. Protein structure classification and databases.
- 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).
