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Introduction To Bioinformatics

Course: B.Sc BiochemistrySubject: Basic of Bioinformatics

Unit: I

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BIOINFORMATICS

• Introduction to bioinformatics• History• Aim scope and importance of bioinformatics• Origin of bioinformatics its application and benefits in life science

industry.• Research areas of bioinformatics.• Fundamentals of Internet: WWW, HTML, URLs Browsers,

Netscape/Opera/Explorer Search Engines: Google, NCBI, PUBMED, entraz

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INTRODUCTION TO BIOINFORMATICS

• Definition: Bioinformatics is an interdisciplinary scientific field that develops methods and software tools for storing, retrieving, organizing and analyzing biological data. As an interdisciplinary field, bioinformatics combines computer Science, statistics, mathematics and engineering to study biological data and processes.

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P. Paulsharma Chakravarthy

WHAT IS BIOINFORMATICS?

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SBIOINFORMATICS DEALS WITH

• Design and implementation of new algorithms and statistics which assess relationship among members of large data sets.

• Analysis and interpretation of various data types, which includes nucleotide and amino acid sequences and structure of protein.

• To develop computational tools and databases that enables efficient analysis, access and management of biologically significant information.

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SAIMS OF BIOINFORMATICS

• Improve content and utility of databases.• Develop better tools for data generation, capture, and annotation.• Develop and improve tools and databases for comprehensive

functional studies.• Develop and improve tools for representing and analyzing sequence

similarity and variation.• Create mechanisms to support effective approaches for producing

robust, exportable software that can be widely shared.

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SGOALS OF BIOINFORMATICS

• Development and implementation of computer programs that enable efficient access to , use and management of various type of information

• Development of new algorithms and statistical measures with which to assess relationships among members of large data.

• Understanding the biological process• Pattern reorganization• Seq. alignment• Gene finding• Assembly• Drug designing• Protein structure alignment• Gene expression• Genome annotation

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SHISTORY OF BIOINFORMATICS

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The IBM 7090 computer, which Margaret Dayhoff used for her early workMargaret Oakley Dayhoff (Ruth Dayhoff's mother), who created the first large scale database of protein sequences, and developed many of the algorithms for analysis of relatedness of proteins, early 1970s

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WHAT ARE THE BIOLOGICAL PROBLEMS?

• What is the role of a particular gene?• Does a particular gene help cause a disease?• How does a drug affect a cell?• Can we insert a gene into corn to protect it against diseases or

pests?• Can we design a drug to accomplish a particular purpose?• Can we build a cell that eats pollution?

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SBIOLOGICAL PROBLEMS THAT COMPUTER CAN HELP

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SWhy Is Bioinformatics So Important?

• Global perspective in experimental design the ability to capitalize on the emerging technology of database-mining - the process by which testable hypotheses are generated regarding the function or structure of a gene or protein of interest by identifying similar sequences in better characterized organisms.

• Although a human disease may not be found in exactly the same form in animals, there may be sufficient data for an animal model that allow researchers to make inferences about the process in humans.

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3.

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S>100,000 species are represented in GenBank

all species 128,941

viruses 6,137

bacteria 31,262

archaea 2,100

eukaryota 87,147

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SNECESSARY SKILL SETS

• Knowledge in Molecular Biology• Statistics• Mathematics (algorithm development)• Communicate biological problems to computer scientists• Working knowledge in bioinformatics tools• Computer proficiency (windows/command line)• Programming Skills• Data administration

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SMOLECULAR BIOLOGY KNOWELEDGE

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5.

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SPROTEIN STRUCUTRE AND FUNCTION

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SAPPLICATIONS OF BIOINFORMATICS

• Knowledge-based drug design, forensic DNA analysis, and agricultural biotechnology.

• Computational studies of protein–ligand interactions• Knowledge of the three-dimensional structures of proteins• This informatics-based approach significantly reduces the time and

cost necessary to develop drugs with higher potency, fewer side effects, and less toxicity than using the traditional trial-and-error approach.

• In forensics, results from molecular phylogenetic analysis have been accepted as evidence

• Genomics and bioinformatics are now poised to revolutionize our healthcare system by developing personalized and customizing

medicine

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• Bioinformatics tools are being used in agriculture as well. • Plant genome databases and gene expression profile analyses have

played an important role in the development of new crop varieties that have higher productivity and more resistance to disease.

APPLICATIONS OF BIOINFORMATICS

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SAPPLICATIONS OF BIOINFORMATICS

9.

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10.

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LIMITATION OF BIOINFORMATICS

• Bioinformatics is Bioinformatics and experimental biology are independent, but complementary, activities.

• Bioinformatics depends on experimental science to produce raw data for analysis. It, in turn, provides useful interpretation of experimental data and important leads for further experimentalresearch.

• Quality of bioinformatics predictions depends on the quality of data and the sophistication of the algorithms being used.

• Sequence data from high throughput analysis often contain errors. If the sequences are wrong or annotations incorrect, the results from the downstream analysis are misleading as well.

• They often make incorrect predictions that make no sense when placed in a biological context. Errors in sequence alignment.

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SSPECIALIZED FIELDS

• Computational Biology• Genomics• Proteomics• Bioprogramming• Cheminformatics• Structural Biology• Systems Biology• Pharmacogenomics

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SMAJOR RESEARCH AREA

• Computational evolutionary biology• Sequence analysis• Genome annotation

• Analysis of regulation• In cancer Analysis of mutations

• Comparative genomics

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Origin of internet

The management and, more importantly, accessibility of the data is directly attributable to the development of the Internet, particularly the World Wide Web (WWW).Originally developed for military purposes in the 60's and expanded by the National Science Foundation in the 80's, scientific use of the Internet grew dramatically following the release of the WWW by CERN in 1992.

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HTML

• The WWW is a graphical interface based on hypertext by which text and graphics can be displayed and highlighted.

• Each highlighted element is a pointer to another document or an element in another document which can reside on any internet host computer. Page display, hypertext links and other features are coded using a simple, cross-platform HyperText Markup Language (HTML) and viewed on UNIX workstations, PCs and Apple Macs as WWW pages using a browser.

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SASSIGNMENT -1--------------------------------10 Marks

1. What is bioinformatics? Why do people consider it as an interdisciplinary subject

2. What are the necessary skills required for bioinformatics study?

3. Write about history of bioinformatics.

4. Describe the application of bioinformatics.

5. What is NCBI?

6. What is Entraz?

7. What is search engine?

8. What is PubMed?

9. Enlist the major research areas of bioinformatics.

10. Give the importance of bioinformatics in biological science.

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STest-1-----------------------------------------------10 Marks 1. What is bioinformatics?-------------------------------------------------1

2. Describe the application of bioinformatics.------------------------2

3. What is NCBI?-------------------------------------------------------------1

4. What is Entraz?-----------------------------------------------------------1

5. What is PubMed?---------------------------------------------------------1

6. Enlist the major research areas of bioinformatics.---------------4

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Web and Books References

• Books Name :

1. Introduction To Bioinformatics by T. K. Attwood

2. BioInformatics by Sangita

3. Basic Bioinformatics by S.Ignacimuthu, s.j.

4. Application of bioinformatics by david mount

• http://en.wikipedia.org/wiki/Bioinformatics• http://bioinformaticsweb.net/applications.html• http://bioinformaticsinstitute.ru/sites/default/files/lapidus_1_0.pdf• History:

http://www.bioinformatics.nl/webportal/background/timeline.html• Links: http://www.ncbi.nlm.nih.gov

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Image References• 1. http://www.esat.kuleuven.be/sista/GGS/images/bioi.jpg• 2. http://www.nature.com/nrg/journal/v1/n3/images/nrg1200-231a-f4.jpg• 3. https://encrypted-tbn2.gstatic.com/images?

q=tbn:ANd9GcSg58MFhqEDknaHb3nHWmkP6mMgUbCjD7ASmqII4befeovn566L9w

• 4. http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/images/central_dogma.gif

• 5. https://encrypted-tbn3.gstatic.com/images?q=tbn:ANd9GcRx8BAquGrTstZrdTzPvvfn2ItAnPVGsjK03JfzMZF6SbpdasCFAw

• 6.https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcRc-CJZHa1e-8Xj78HMvWR-FNzw0KF4tEHrmH8clOcCzlOeYT3i

• 7. http://upload.wikimedia.org/wikipedia/commons/e/e6/Spombe_Pop2p_protein_structure_rainbow.png

• 8. https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcSHmWGzX5jd6PvwdiaYdxnGcCKOXjmxBmoz_YiE7L1xLNvzAkQvITmdSrRy

• 9. & 10.Book: Basic Bioinformatics by S.Ignacimuthu, s.j.