Detailed Notes on Bioinformatics (Zoology Course ZOOL4128)
Course Title: Bioinformatics
Course Code: ZOOL4128
Credit Hours: 3 (1+2)
Objectives:
- To introduce fundamental bioinformatics concepts and problem-solving strategies.
- To explain tools used for bioinformatics solutions and the theory behind them.
Introduction to BI
Bioinformatics (BI) is the use of computational tools to manage, analyze, and interpret biological
data. It has applications in genomics, proteomics, drug discovery, and evolutionary biology. History
of BI includes the Human Genome Project and development of biological databases. Uses include
protein and gene data analysis. Comparison of BI with experimental tools shows that BI is faster and
cost-effective for large data analysis.
Basic principles of computing in bioinformatics
This involves understanding how biological data is acquired and stored. Major biological databases
include:
- DDBJ (DNA Data Bank of Japan)
- NCBI (National Center for Biotechnology Information)
- EMBL (European Molecular Biology Laboratory)
These databases store nucleotide sequences, protein sequences, and gene expression data.
Short introduction to DNA, RNA and protein
DNA and RNA are nucleic acids composed of nucleotides. Proteins are made of amino acids.
Understanding sequences helps in analyzing structure and function. BI tools are used for:
- Analyzing sequences
- Predicting structure
- Understanding functions of proteins
Retrieving protein sequences from database (FASTA)
FASTA format is a standard for representing nucleotide or peptide sequences. Tools used:
- BLAST: Finds regions of similarity between sequences
- CLUSTALW: For multiple sequence alignment
- PROTPARAM: Computes physicochemical properties
- PSSP: Predicts secondary structure
- NETPHOS: Predicts phosphorylation sites
These tools help in 3D structure prediction and identifying post-translational modifications (PTMs).
Enzyme classification
Enzymes are classified based on the reactions they catalyze. Databases store information on
enzyme functions, structures, and pathways. Retrieval of enzyme-related data is essential in
studying metabolism and drug targets.
Short introduction to DNA/RNA
Covers the structure of DNA/RNA, the genetic code, and sequence analysis. Tools are used to
understand mutations, codon usage, and regulatory sequences.
Retrieving the DNA sequence from database
Involves:
- Identifying restriction sites (used in cloning)
- Predicting secondary structure (e.g., hairpins in RNA)
- Aligning DNA sequences to find evolutionary relationships or mutations
PRIMER Designing for PCR
PCR primers are short sequences designed for DNA amplification. Tools include:
- PRIMER3+: Custom primer design
- PRIMER-BLAST: Combines primer design with BLAST search
- OLIGO-CALC: Calculates properties like melting temperature
Good primer design ensures specificity and efficiency of PCR.
Short Introduction to Proteomics and Genomics
Proteomics studies the protein content of a cell, while genomics focuses on the genome.
Applications include:
- Drug development
- Disease diagnosis
- Understanding cellular functions
Bioinformatics helps integrate large data sets from both fields for systems biology research.
