Bioinformatics. Introduction and Application Dr. Ghasemian Safaei. Outline. Bioinformatics Definition Evolution of Bioinformatics Bioinformatics History Application of Bioinformatics Procedures and Tools of Bioinformatics. Definition .
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Introduction and Application
Evolution of Bioinformatics
Application of Bioinformatics
Procedures and Tools of Bioinformatics
The application of computer scienceand information technologyto the field of biologyandmedicine.
Mathematics and Statistics
All aspects of gathering, storing, handling, analyzing, interpreting and spreading vast amounts of biological information in databases.
Biological structure, molecular structure,
Computational management and analysis of biological information: genes, genomes, proteins, cells, ecological systems, medical information, ......
A major activity in bioinformatics is to develop software tools to generate useful biological knowledge
The Core of Bioinformatics to date tools to generate useful biological knowledge
to infer relationships between components of complex biological systems
1-Frederick tools to generate useful biological knowledgeGriffith British microbiologist
2-Oswald Theodore Avery (1877-1955) Colin MacLeod Maclyn McCarty
3-Alfred Hershey (1908-1997) ,Martha Chase (1930- )
New applications ….. Molecular biotechnology
Since the Phage Φ-X174 was sequenced in 1977,
The Institute for Genomic Research to sequence the first bacterial genome, Haemophilusinfluenzae).
Computationalgene finding to search for protein-coding genes, RNA genes, and other functional sequences within a genome
In the context of genomics, annotation is the process of marking the genes and other biological features in a DNA sequence.
The first genome annotation software system was designed in 1995 by Owen White, who was part of the team at The Institute for Genomic Research.
Evolutionary biology is the study of the origin and descent of species, as well as their change over time.
Informatics has assisted evolutionary biologists in several key ways; it has enabled researchers to find the new species .
The growth in the number of published literature makes it virtually impossible to read every paper, resulting in disjointed sub-fields of research.
Literature analysis aims to employ computational and statistical linguistics to mine this growing library of text resources.
abbreviation recognition – identify the long-form and abbreviation of biological terms,
named entity recognition – recognizing biological terms such as gene names
protein-protein interaction – identify which proteins interact with which proteins from text
The area of research draws from statistics and computational linguistics.
The expression of many genes can be determined by measuring mRNA and protein levels with multiple techniques .
Information processing in cells tools to generate useful biological knowledge
Protein microarrays and high throughput (HT) mass spectrometry (MS) can provide a snapshot of the proteins present in a biological sample.
Regulation is the complex orchestration of events starting with an extracellular signal such as a hormone and leading to an increase or decrease in the activity of one or more proteins. Bioinformatics techniques have been applied to explore various steps in this process.
In cancer, the genomes of affected cells are rearranged in complex or even unpredictable ways. Massive sequencing efforts are used to identify previously unknown point mutations in a variety of genes in cancer.
The core of comparative genome analysis is the establishment of the correspondence between genes (orthology analysis) or other genomic features in different organisms
Network analysis seeks to understand the relationships within biological networks such as metabolic or protein-protein interaction networks. Although biological networks can be constructed from a single type of molecule or entity (such as genes),
network biology often attempts to integrate many different data types, such as proteins, small molecules, gene expression data, and others, which are all connected physically and/or functionally.
Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks) to both analyze and visualize the complex connections of these cellular processes.
Computational technologies are used to accelerate or fully automate the processing, quantification and analysis of large amounts of high-information-content biomedical imagery.
Protein structure prediction is another important application of bioinformatics. The amino acid sequence of a protein, the so-called primary structure, can be easily determined from the sequence on the gene that codes for it
GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms.
GenBankcontinues to grow at an exponential rate, doubling every 10 months.
Release 134, produced in February 2003, contained over 29.3 billion nucleotide bases in more than 23.0 million sequences.
GenBankis built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers.
The GenBank direct submissions group has processed more than 50 complete microbial genomes since 1996.
These genomes are relatively small in size compared with their eukaryotic counterparts, ranging from five hundred thousand to five million bases. Nonetheless, these genomes can contain thousands of genes, coding regions, and structural RNAs; therefore, processing and presenting them correctly is a challenge.( 2007)
Iran Bioinformatics Center (IBC) is the only academic center in Iran working on Bioinformatics.
Although there are some independent research groups such as Bioinformatics and Biomathematics UnitinMazandaran University of Medical Sciences working on Bioinformatics but IBC is a part of Institute of Biochemistry and Biophysics (IBB) in Tehran University. IBC offers a Ph.D. program for Bioinformatics.
The Iranian Bioinformatics Society (IBIS)
The TMU Bioinformatics group