(BT05134) COMPUTATIONAL MOLECULAR BIOLOGY

Unit I: Computational Molecular Biology-I
Natural Biological principles behind BLAST,
Unit II: Computational Molecular Biology-II
FASTA, MSA {Dynamic Programming, CLUSTAL W (Des Higgins)} Karlin - ALshultzl
E -values Matrices PAM, BLOSOM.
Unit III: Methods in PHYLOGENEIC Analysis
CLADISTICS,PHENETICS, EVOLUTIONARY PHYLOGENETICS
UNIT-IV: Maximum Likelihoods
Models of evolution 1) JUKES and CANTOR MODEL 2) KIMURA-2- PARAMETER
MODEL 3) LOGDET METHOD.
Unit V: Genomics
Sequence assembly and gene identification. Homology based gene prediction.
Restriction mapping analysis, coding region identification. SNPs and applications.
Methods of studying gene expression, EST approach,
Unit-VI Micro arrays
a)Basics of Micro array
b) Primer on comparative Genomics.
Unit-VII: Proteomics I
Introduction to proteins. Protein identification, structure and function determination.
Structure comparison methods. Prediction of secondary structure from sequence.
Secondary structure based fold and classification (CATH and SCOP), CASP
Experiments yearly updates 2001-2005
Unit VIII: Proteomics II
Protein homology modeling, Protein threading. Protein ab initio structure prediction.
Protein design emphasis on structural Bioinformatics.
TEXT BOOKS:
1. David W Mount. Bioinformatics- Sequence and genome analysis. CSHL Press.
2. S. Sahai, Genomics and Proteomics, Functional an Computational Aspects,
Plenum Publications, 1999.
REFERENCES:
1. Moody P C E and A J Wilkinson. Protein Engineering. IRL Press.
2. Creighton T E, Proteins. Freeman W H. Second edition 1993.
3. Journal BIOINFORMATICS (Oxford University).
4. BRANDOND TOOZE – Proteomics.