Sci 20: Bioinformatics Lecture 1 PDF

SCI 20: Bioinformatics Lecture #1: The Beginning of Bioinformatics Chuckcris Tenebro, M.Sc. Instructor Iloilo Science and Technology University 1  Origins of Bioinformatics 1. Margaret Dayhoff - Known as...

SCI 20: Bioinformatics Lecture #1: The Beginning of Bioinformatics Chuckcris Tenebro, M.Sc. Instructor Iloilo Science and Technology University 1  Origins of Bioinformatics 1. Margaret Dayhoff - Known as the "mother/founder of bioinformatics" - Developed the first protein sequence database and created the PAM (Point Accepted Mutation) matrices. PAM - a single amino acid substitution in a protein that has been accepted by natural selection and does not disrupt the protein's function 2. Richard Eck - Pioneered early research in molecular evolution. 3. Robert Ledley - Introduced automated approaches in molecular biology and computation. 2  Origins of Bioinformatics 1. Margaret Dayhoff Margaret Dayhoff is known as the founder of bioinformatics. She pioneered key applications of mathematics and computational techniques to the sequencing of proteins and nucleic acids. Her development of “evolutionary trees” reveals that genes commonly found in normal body tissue cells are closely related to those in many cancer cells. https://www.whatisbiotechnology.org/index.php/people/summary/Dayhoff 3  PAM Matrices These are scoring matrices used in sequence alignment that reflect the likelihood of one amino acid being replaced by another over evolutionary time. Used in algorithms for protein sequence alignment. Aids in analysis of phylogenetic trees. Helps predict homologous relationships between proteins. 4  Historical Significance These pioneers in bioinformatics laid the groundwork for combining computational methods with biological data analysis. Dayhoff’s Atlas of Protein Sequence and Structure was a major milestone in bioinformatics history. ▪ The atlas represents one of the earliest comprehensive efforts to catalog and analyze protein sequences and their structures. ▪ The atlas introduced the concept of Point Accepted Mutations (PAM) and the associated PAM matrices, which are widely used in sequence alignment to understand evolutionary relationships. ▪ By analyzing protein sequences, the atlas helped trace evolutionary changes and relationships between proteins from different organisms. 5  What is Bioinformatics? Bioinformatics is the application of computational tools and techniques to analyze biological data. It Integrates molecular biology, computer science, mathematics, and statistics. Bioinformatics includes the following fields: ▪ Genome annotation and sequence analysis ▪ Structural bioinformatics: 3D modeling of biomolecules ▪ Comparative genomics and systems biology Bio infor ma ti cs Biology Information Maths Statistics Computer Technology Science 6 Bioinformatics vs. Computational Biology Bioinformatics focuses on the management, analysis, and visualization of biological data. Computational biology emphasizes theoretical modeling and simulation. 7 “Bio-” in Bioinformatics 8 “-informatics” in Bioinformatics 9  Bioinformatics in the Central Dogma of Molecular Biology DNA RNA Protein DNA Sequencing RNA Sequencing Visualizing Protein Identifying DNA Identifying tissue-specific 3D Structure Mutations gene expression. 10  Primary Goals of Bioinformatics To organize and analyze biological data in meaningful ways. Enable predictions about biological function and behavior. Develop computational tools for research in genomics and proteomics. Examples: ▪ Identification of disease-related genes ▪ Prediction of protein structure and function ▪ Tracing evolutionary relationships among organisms Applications: personalized medicine, agriculture, and drug development. 11 Tools and Techniques in Bioinformatics Essential Tools and Algorithms 1. Sequence Alignment ▪ Identifies similarities and evolutionary relationships ▪ Tools: BLAST (Basic Local Alignment Search Tool), ClustalW 2. Protein Structure Prediction ▪ Predicts the 3D structure of proteins based on sequences ▪ Tools: SWISS-MODEL, AlphaFold 3. Phylogenetics ▪ Reconstruct evolutionary trees ▪ Tools: MEGA, PhyML 12  BLAST (Basic Local Alignment Search Tool) 13 SWISS-MODEL 14  MEGA (Molecular Evolutionary Genetics Analysis) 15 Tools and Techniques in Bioinformatics Key Databases 1. GenBank - Repository of DNA sequences 2. UniProt - Comprehensive protein sequence and functional information 3. PDB (Protein Data Bank) - 3D structural data of biomolecules Applications: Gene prediction functional annotation Biological network analysis 16 GenBank 17 UniProt 18 PDB (Protein Data Bank) 19 Pioneering Databases in Bioinformatics Dayhoff’s Contributions ▪ Protein sequence database development ▪ PAM matrices, crucial for understanding evolutionary substitution rates National Center for Biotechnology Information (NCBI) ▪ Hosts GenBank, a key DNA sequence database ▪ Provides tools like BLAST for sequence analysis European Bioinformatics Institute (EBI) ▪ Maintains databases like UniProt and Ensembl 20  Summary Bioinformatics combines biology with computational sciences. Early pioneers established crucial tools and methods still in use today. Current applications span medicine, agriculture, and evolutionary studies. 21 Decoding Your Questions… 22