What is Bioinformatics? (1)
Bioinformatics -use of computer to store, analysis
and manipulate biological information
What is Bioinformatics? (2)
-manage and manipulate sequence data-use that sequence data in the analyses of
gene, protein, and DNA function-designing novel and incisive algorithms-create new/maintain existing databases
of information-allowing open access to the records held
within them
Onset of Bioinformatics
-Huge advances in the fields of molecular biologyand genomics especially after Human Genome Project
-This cause massive amount of biological information available
What is developed?
-Biological databases are consistent data that are stored in a uniform and efficient manner
-These databases contain data from a broad spectrum of molecular biology area
-Primary databases contain -information and annotation of DNA protein
sequences
-DNA and protein structures and DNA and protein expression profiles
Genbank
-First database setup to store DNA sequence data, set up In 1982
-manage by National Centre Biotechnology Information
-currently holds about 17 billion bases from more than 100,000 organisms
-Each of the sequences are given an ID number for easy identification in the database
http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
EMBL (European Molecular Biology Laboratory) Nucleotide Sequence Database
-a comprehensive database of DNA and RNA sequences
-manage by European Bioinformatics Institute (EBI)
-information collected from the scientific literature and patent applications
-supported by 17 countries in Western Europe -currently contains nearly more than 10 million
baseshttp://www.ebi.ac.uk/embl/
SwissProt:
-a database of protein sequence, function and structure
-manage by European Bioinformatics Institute -provides a high level of integration with other datab
ases -a very low level of redundancy (means less identical
sequences are present in the database)http://www.ebi.ac.uk/swissprot/
EC-ENZYME:
The 'ENZYME' data bank contains the following data for a characterized enzyme:
-EC number -Recommended name and Alternative names-Catalytic activity-Cofactors-Pointers to the SWISS-PROT entry that
correspond to the enzyme-diseases associated with a deficiency of the
enzyme
Protein Data Bank
-manage by Research Collaboratory for Structural Bioinformatics (RCSB)
-a collection of all publicly available 3D structures of proteins, nucleic acids, carbohydrates
-variety of other complexes experimentally determined by X-ray crystallography and NMR
http://www.rcsb.org/pdb/
Structural Analysis
-DNA sequences that encode proteins with specific function
-Researchers predict the 3D structure using protein or molecular modeling
-Experimentally determined protein structures (templates) are used
-to predict the structure of another protein that has a similar amino acid sequence (target)
Algorithm
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
PROSPECT
-Protein Structure Prediction and Evaluation Computer Toolkit
-a protein-structure prediction system -It construct a 3-D model of proteins by protein threading- Protein threading Algorithms for protein fold recognitionhttp://www.bioinformaticssolutions.com/pro
ducts/prospect.php
Advantages in Protein Modeling
-Examining a protein in 3D allows for greater understanding of protein functions
-providing a visual understanding that cannot always be conveyed through still photographs or descriptions
Homology and Similarity Tools
-Homology and Similarity Tools are use to analyses similarity between two sequence or structure
-the degree of similarity between two sequences can be measured
-applied in evolutionary studies
BLAST (Basic Local Alignment Search
Tool)
-homology and similarity tools-develop by NCBI -Search programs designed for the
Windows platform -used to perform fast similarity
searches for protein or DNA -users can retrieve results and format
their results in different format
Molecular Medicine
-Most of the disease has a genetic component and environmental component
-we can search for the genes directly associated with different diseases
-begin to understand the molecular basis of these diseases more clearly
-better treatments, cures and even preventative tests to be developed
Personalized Medicine
-Development of the field of pharmacogenomics -study of how an individual's genetic inheritance
affects the body's response to drugs -At present, doctors have to use trial and error to
find the best drug to treat a particular patient-In the future, doctors will be able to analyze a
patient's genetic profile and prescribe the best available drug therapy and dosage from the beginning
Microbial genomic application
-MGP (Microbial Genome Project) to sequence genomes of bacteria
-useful in energy production, industrial processing and toxic waste reduction
-scientists can begin to understand these microbes at a very fundamental level
-isolate the genes that give them their unique abilities to survive under extreme conditions
Waste clean up
-Deinococcus radiodurans is known as the world's toughest bacteria
-the most radiation resistant organism known
-Scientists are interested in this organism because of its potential usefulness in cleaning up waste sites that contain radiation and toxic chemicals
Evolutionary studies
-sequencing of genomes from different organism
-evolutionary studies can be performed to determine the tree of life
-find last universal common ancestor
Impact of Bioinformatics 1
-Bioinformatics leads to advances in understanding basic biological processes, treatment, and prevention of many genetic diseases
-Bioinformatics has transformed the discipline of biology from a purely lab-based science to an information science as well
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