Friday, 20 September 2013

MTI - 506 BIOINFORMATICS (II)

UNIT 1: Introduction to Biological Databases
Database : Types, Overview of Biological Databases and Information retrieval
from biological databases for example (Nucleic acid databases: Genbank, Protein
Databases- Swissprot) Sequence Formats, Sequence storage, Sequence
submission to sequence Database.

UNIT 2: Pairwise Sequence Alignment
Alignment Types: Local alignment, Global alignment, Scoring matrices- PAM,
BLOSUM, Gaps, Types of Gaps. Dot Plots. Dynamic programming Approach:
Needleman and Wunsch Algorithm, Smith and waterman Algorithm, Viterbi
Algorithm, Heuristic Approach: BLAST, FASTA.

UNIT 3: Multiple Sequence Alignment:
Exhaustive Algorithm- Divide and Conquer alignment, Heuristic Algorithm:
Progressive Alignment- ClustalW, Tcoffee, Iterative Alignment- PRRN, Block
based method- Match-Box, DIALIGN2

UNIT 4: Introduction to Protein Structure Prediction
Secondary structure prediction for Globular and Trans-membrane proteins, 3DProtein
Structure file format: PDB, mmCIF, MMDB, Methods of Tertiary
structure prediction: Threading and fold recognition methods, Homology
modeling, Fold recognition databases.


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