BT-401 (Bioinformatics)
Scope & Objective:
The aim of the subject is to create a knowledge database of genes and proteins, data mining, understanding protein-protein interaction, binding site prediction, homology modeling, and finding genes and co-regulated genes.
UNIT I
Introduction
Sequence database of genes, nucleic acids, and proteins
Nucleotide sequence database of nucleic acids
Amino acid sequence database of proteins
Structure database
Gene library data bank
Protein data bank (PDB)
Molecular modeling database at NCBI
Raw database and processed database
Data mining
Data storage and retrieval
Querying in database and tools for querying - BLAST, FASTA
UNIT II
Software-based sequence analysis and sequence alignment
Gene finding
Hidden Markov Models (HMM)
Prediction of co-regulated genes
Annotation of protein sequences
Substitution matrices
Local, global, and multiple sequence alignment
Clustering
Prediction
Protein-protein interaction
Protein chips
Searching in the database
Binding site prediction
Wisconsin package
Analyzing sequence with WP programs
Monitoring programs
Troubleshooting problems
Extension of Wisconsin package
Annotating sequences
Displaying and saving annotations in Sequence Laboratory Editor
Information retrieval from biological databases
Medical database
UNIT III
Phylogenetic data analysis
Elements in phylogenetic models
Phylogenetic tree analysis
Searching for trees
Phylogenetic software PHYLIP and application
Structural database
Protein structure database
Modular nature of proteins
Homology modeling
Comparison and superposition of structures
Alignment studies
Determining substituted models
Progressive alignment methods
Database similarity searching
Low complexity regions
Repetitive elements
Structural motives and patterns
UNIT IV
Masking repetitive DNA
Codon bias detection
Detecting functional sites
Finding RNA genes
Predictive methods using gene sequences
Physical properties based on sequences
Plasmid mapping
Primer design for PCR
Restriction mapping
DNA chips
Comparative genomics
Cancer gene maps and comparison study
Prediction
Comparison of distance matrices
Searching for patterns and motifs
Evolution of protein structure and sequences by comparing different organisms
Human genome introduction
Tools for analysis
Gene finding
Probing with ESTs
Exon microarray
Database
Functional genomics
Textbooks & Reference:
1. Sensen, C.W., "Essentials of Genomics and Bioinformatics," John Wiley and Sons, 2002
2. Attwood, T. and Parry-Smith, D., "Introduction to Bioinformatics," Prentice Hall, 1999
3. Baxevanis, A.D. and Ouellette, B.F.F., "Bioinformatics: A Practical Guide to the Analysis of Genes and Protein," Wiley-Interscience, 2001
4. "Bioinformatics: A Biologist's Guide to Computing and the Internet" by Stuart M. Brown, NKU Medical Center, NY USA, 2000.