BIOINFORMATICS

 

Course Contents:

Unit 1: Foundations to Bioinformatics

Foundations to bioinformatics – Evolution, similar macromolecular components, constancy of gene number and core proteome in closely related organisms

Bioinformatics data – nucleic acid sequence, protein sequence, protein structure, genomic, proteomic and metabolomic information

Bioinformatics databases – types, design, file formats, access tools with examples

Bioinformatics tools and Resources – free online tools, downloadable free tools, software packages, internet,

 Bioinformatics books and Journals, Bioinformatics web-portals

 

Unit 2: Comparison methods in bioinformatics

Dot-matrix comparison

Basics of sequence alignment - match, mismatch, gaps, scoring alignments, gap penalty, protein vs DNA alignment

Pairwise alignment algorithms – Needleman and Wunch algorithm, Smith Watermann algorithm

Multiple sequence alignment algorithms – progressive alignment algorithms, Iterative alignment algorithms

Pair wise alignment based heuristic algorithms - Blast algorithm, FASTA algorithm

Multiple sequence alignment based databases searching: Consensus sequence, patterns, profiles

PAM and BLOSUM Matrices
 

Unit – 3: Genomic and proteomic Bioinformatics

Bioinformatics for genome sequencing

EST Clustering and analyses

Finding genes in prokaryotic and eukaryotic genomes: open reading frames, contents, signals

Regulatory sequence analysis: core and distal promoter sequences, transcription factor binding sites

Bioinformatics for Genome maps and markers

Bioinformatics for understanding Genome variation

Protein structure prediction and classification

Bioinformatics in support of Proteomic research

Unit - 4: Applications of Bioinformatics

Medical application of Bioinformatics – disease genes, drug targets, pharmacogenomics, drug designing

Structural biology - Homology modeling

Bioinformatics for micro array designing and transcriptional profiling

Bioinformatics for metabolic reconstruction

Bioinformatics for phylogenetic analysis