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Bioinformatics ppt
This document provides an overview of bioinformatics and some of its key applications. It discusses how bioinformatics is an interdisciplinary field that uses computer science, statistics and other approaches to analyze large amounts of biological data. It notes that bioinformatics has become necessary due to the explosion of genomic data from projects like the Human Genome Project. Some of the goals and uses of bioinformatics mentioned include uncovering biological information from data, applications in molecular medicine, agriculture and environmental science. The document also provides brief descriptions of structural bioinformatics, common biological databases, MASCOT database searching, and scoring schemes used in bioinformatics.
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Overview of bioinformatics, its search tools like MASCOT and UniProt, setting the stage for further discussion.
Definition and significance of bioinformatics. Highlights interdisciplinary nature and areas where it contributes significantly.
Focuses on structural bioinformatics and notable databases like GenBank and UniProt for research and data.
Explains MASCOT’s role in interpreting mass spectral data for protein identification and its capabilities.
Details the MOWSE algorithm used by MASCOT, scoring schemes, and parameters for effective database searching.
Final slide thanking the audience, closing the presentation.
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Bioinformatics ppt
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- 3. What is bioinformatics? ITis an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data
- 5. Why Bioinformatics isnecessary? The need for bioinformatics has arisen from the recent explosion of publicly available genomic information, such as resulting from the Human Genome Project. Gain a better understanding of gene analysis, taxonomy, & evolution. To work efficiently on the rational drug designs and reduce the time taken for the development of drug manually
- 6. Goals of Bioinformatics Touncover the wealth of Biological information hidden in the mass of sequence, structure, literature and biological data. It is being used now and in the foreseeable future in the areas of molecular medicine. It has environmental benefits in identifying waste and clean up bacteria. In agriculture, it can be used to produce high yield, low maintenance crops.
- 7. Where Bioinformatics helps? In Experimental Molecular Biology In Genetics and Genomics In generating Biological Data Analysis of gene and protein expression Comparison of genomic data Understanding of evolutionary aspect of Evolution Understanding biological pathways and networks in System Biology In Simulation & Modeling of DNA, RNA & Protein
- 8. Bio Informatics keyareas
- 9. Structural Bioinoformatics Predictionof structure from sequence ◦ secondary structure ◦ homology modelling, threading ◦ ab initio 3D prediction Analysis of 3D structure ◦ structure comparison/ alignment ◦ prediction of function from structure ◦ molecular mechanics/ molecular dynamics ◦ prediction of molecular interactions, docking Structure databases (RCSB)
- 10. List of Database DNA Data Bank of Japan (National Institute of Genetics) EMBL (European Bioinformatics Institute) GenBank (National Center for Biotechnology Information) UniProt Universal Pesource (EBI, Swiss Institute of Bioinformatics, PIR) Swiss-Prot Protein Knowledgebase (Swiss Institute of Bioinformatics) National Center for Biotechnology Information (NCBI) NIM,USA
- 11. MASCOT Search Simple MS– molecular weight of peptide mixture. MS/MS (Tandem MS) – sequence structural information by recording the fragment ion spectrum of peptide.
- 12. PURPOSE OF MS: Elemental composition. Masses of particles of molecules. Identify unknown compounds. Isotopic Composition.
- 13. Mascot isa software package from Matrix Science (www.matrixscience.com) that interprets mass spectral data into protein identities. It uses mass spectrometry data to identify proteins from primary sequence databases. The experimental mass values are then compared with calculated peptide mass by applying cleavage rules to the entries in a comprehensive primary sequence database. If unknown protein is present, we will get precise entry otherwise pull out those entries which exhibit the closest homology(related species).
- 15. Algorithm used.. Program MASCOTis based on the MOWSE algorithm; this program also evaluates a possibility of random matching of experimental and theoretical peptide masses.
- 16. Two Mascot Choices MatrixSciences offers two choice for users: A free, open access web-based system for occasional (1-10) queries. A locally installed version for heavy use or highthroughput MS (100’s queries/day)
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- 20. Parameters used indatabase searching Database searched Taxonomy Enzyme Missed cleavages Fixed versus variable modifications (PTMs)
- 21. SCORING SCHEMES PROBABILITYBASED SCORING Mascot incorporates a probability based implementation of the Mowse algorithm The total score is the absolute probability that the observed match is a random event. Advantages : Different types of matching (peptide masses and fragment ions) can be combined in a single search. Scores from different searches and on different databases can be compared. Search parameters can be optimised more readily by iteration.
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