bio-bio-1 team advisor: dr. supten sarbadhikari members: fokhruz zaman zohirul alam tiemoon saddam...
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Bio-bio-1 TeamAdvisor:
Dr. Supten Sarbadhikari
Members:
Fokhruz ZamanZohirul Alam TiemoonSaddam HossainFarjana Khatun
Bioinformatics
2 (c) Mark Gerstein, 1999, Yale, bioinfo.mbb.yale.edu
Original definition (1979 by Paulien Hogeweg):“application of information technology and computer science to the field of molecular biology”
Biological Data + Computational
Calculation
Why Use of BioinformaticsWhy bioinformaticsTo Find an answer quickly
- in-silicobiology is faster than in-vitroMassive amounts of data to analyse
• Need to make use of all information• Not possible to do analysis by hand• Can’t organise and store information only using lab
note books• Automation is key
All results of computer analysis should to be verified by biologists
Data Type Data Size Topics
Raw DNA sequence
8.2 million sequences(9.5 billion bases)
Separating coding and non-coding regionsIdentification of introns and exonsGene product predictionForensic analysis
Protein sequence
300,000 sequences(~300 amino acidseach)
Sequence comparison algorithmsMultiple sequence alignments algorithmsIdentification of conserved sequence motifs
Macromolecularstructure
13,000 structures(~1,000 atomiccoordinates each)
Secondary, tertiary structure prediction3D structural alignment algorithmsProtein geometry measurementsSurface and volume shape calculationsIntermolecular interactions
Data Type Data Size Topics
Genomes 40 complete genomes(1.6 million –3 billion bases each)
Characterisation of repeatsStructural assignments to genesPhylogenetic analysisGenomic-scale censuses(characterisation of protein content, metabolic pathways)Linkage analysis relating specific genes to diseases
Gene expression
largest: ~20 timepoint measurementsfor ~6,000 genes
Correlating expression patternsMapping expression data to sequence, structural andbiochemical data
Quantity of each type of data that is currently (August 2000) available
Why Use of BioinformaticsBiological data are being produced at a unusual
rate. On average, these databases are doubling in size
every 15 months To bring together and store vast
amounts of information from •Lab equipment and experiments•Computer Analysis•Human Analysis•Make visible to the world’s scientists
Without Bioinformatics, Human Genome Project could not have been achieved !!!
Goals of Bioinformatics Development and implementation of tools that enable efficient access to, and use and management of, various types of information.
Development of new algorithms and statistics with which to assess relationships among members of large data sets, such as methods to
- locate a gene within a sequence,- predict protein structure and/or function,- uncover the wealth of biological information
hidden in the mass of data- obtain a clear insight into the fundamental biological process of organisms.- identify malfunctions in these processes which lead to diseases- find approaches to improving drug discovery.
Bioinformatics Databases• Public databases are the most important
entity in bioinformatics• Store knowledge about
- Sequence e.g. EMBL- Structure e.g. PDB- Pathways e.g. KEGG- Interactions e.g. DIP- Diseases e.g. OMIMAnd many others …
• Can be searched in a variety of ways e.g. keyword, pattern, sequence
Cycle of Life
KKAVINGEQIRSISDLHQTLKKWELALPEYYGENLDALWDCLTGVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIE
Evolution
Sequence
Structure
Function
Ligand
Central Paradigm of Bioinformatics
Biochemical Function
Molecular Structure
Genetic Informatio
n
Symptoms
Real world of Bioinformatics1. Molecular medicine
More drug targetsPersonalized medicinePreventative medicineGene therapy
2. Microbial genome applicationsWaste cleanupClimate changeAlternative energy sourcesBiotechnologyAntibiotic resistanceForensic analysis of microbesThe reality of bio-weapon creationEvolutionary study
3. AgricultureCropsInsect resistanceImprove nutritional qualityGrow crops in poorer soils and that are drought resistant
4. Animals
5. Comparative studies
Bioinformatics Challenges
Biological Redundancy and multiplicity
Different sequences with similar structures
Difference structures with similar sequences
Organisms with similar genes
Multiple functions of single gene
Grouping of genes in pathways
Significance of relationships and similarities
Lack of Data
Referenceshttp://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html What is bioinformatics? An introduction and overview, N.M.
Luscombe, D. Greenbaum, M. Gerstein. Department of Molecular Biophysics and Biochemistry Yale University, New Haven, USA
Introduction to BioinformaticsIntroduction Bioinformatics, Stephen Taylor
Intro to BioInformatics, Esti Yeger-Lotem, Doron Lipson, Lecture I: Introduction & Text Based Search
Emerging Areas in BIOINFORMATICS, Dr. Gulshan Wadhwa, National Seminar on "Intellectual Property Rights in Bioinformatics and Biotechnology” September 15 2005 Bioinformatics Centre, Pondicherry University
BIOINFORMATICS Introduction, Mark Gerstein , Yale University bioinfo.mbb.yale.edu/mbb452a
http://www.cs.usfca.edu/~pfrancislyon/resources/cs686_01_intro.pdf
…………….. Some downloaded ppt.
Some Web Related to Bioinformatics
http://bio-bio-1.wikispaces.comhttp://www.dnalc.org/http://www.bioinformaticsatschool.eu/