Bioinformatics Lecture 1 PDF

Bioinformatics BIO417 Lecture 1 Bioinformatics: What and Why? Prepared by Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics ...

Bioinformatics BIO417 Lecture 1 Bioinformatics: What and Why? Prepared by Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli  Bioinformatics: Definition Associate Professor of Biochemistry and Molecular Genetics  The term “bioinformatics” have been first used in the mid-1980s to describe application of technology in life sciences.  The definition was at that time very general, covering everything from robotics to artificial intelligence.  Later, bioinformatics came to be defined as “the use of computers to retrieve, process, analyze, and simulate biological data”.  The study of DNA sequence of a living organism is the core of bioinformatics.  Scientists could provide more clarifications for bioinformatics as “the field that develops methods and software tools for understanding biological data”.  Bioinformatics: Overview  In general, it is highly interdisciplinary, requiring knowledge of computer, biological, mathematical, physical, chemical, biotechnology, medicine, and pharmacology sciences. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Bioinformatics: Overview  The handling and analysis of DNA sequences remains one of the prime tasks of bioinformatics.  This topic is divided into two parts:  Functional genomics, which seeks to determine the role of the sequence in the living cell, either as:  transcribed and translated unit.  regulatory motif; such as promoter site or a piece of small interfering RNA.  Comparative genomics, in which the sequences from different organisms, or even different individuals, are compared to determine correlations with disease. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Bioinformatics fields  Genomics:  Gene identification.  Gene annotation.  Transcriptomics:  Gene expression.  Proteomics:  Protein structure prediction.  Metabolomics:  Metabolic process & pathways Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics Importance of Bioinformatics  Big data describes large and diverse datasets that are huge in volume and rapidly grow in size over time.  Big data is used in machine learning, bioinformatics, and other advanced analytics.  Importance of Bioinformatics:  Bioinformatics is an interdisciplinary field that combines biology, computer science, and statistics to explore the mysteries of living systems.  By integrating data from different sources, bioinformatics provides a comprehensive view of biological processes, which helps in drug development and disease diagnosis.  It enables researchers to analyze vast amounts of biological data that would be impossible to process manually. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics What is biological databases?  Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high- throughput experiment technology, and computational analysis.  They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics.  Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics Types of biological databases  Primary databases:  They are also called as archival database.  They are populated with experimentally derived data such as nucleotide sequence or protein sequence.  Experimental results are submitted directly into the database by researchers, and the data are essentially archival in nature.  Once given a database accession number,  Examples: the data in primary databases are never  GenBank and NCBI (nucleotide changed: they form part of the scientific sequence). record.  Gene Expression Omnibus (GEO) database (functional genomics data). Sequencing DNA  Protein Data Bank (PDB; coordinates AATGCGTATAAGGC of three-dimensional structures). Amino acids DMPVERILEALAVE Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli Types of biological databases Associate Professor of Biochemistry and Molecular Genetics Types of biological databases  Secondary databases:  These databases comprise data derived from the results of analyzing primary data.  Secondary databases often draw upon information from numerous sources, including other databases, and scientific literature.  They are highly curated, often using a complex combination of computational  Examples: algorithms and manual analysis.  UniProt database (sequence and  Secondary database is better and contains functional information on proteins). more valuable knowledge compared to the  Ensembl database (variation, primary database. function, regulation and more layered  Interpretation depends on deriving new onto whole genome sequences). knowledge from the public record of  VarSome is a variant knowledge science. community, data aggregator and variant data discovery tool. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics Types of biological databases  Composite databases:  The data entered in these types of databases are first compared and then filtered based on desired criteria.  The initial data are taken from the primary database, and then they are merged based on certain conditions.  It helps in searching sequences rapidly.  Examples:  Cytoscope.  String database.  Malacards.  Genecards.  GeneMANIA.  PROTTER. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics