introduction to bioinformatics

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Introduction To Bioinformatics
Course: B.Sc Biochemistry
Subject: 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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BIOINFORMATICS 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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AIMS 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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GOALS 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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HISTORY OF BIOINFORMATICS

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The IBM 7090 computer, which Margaret Dayhoff used for her
early work
Margaret 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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BIOLOGICAL PROBLEMS THAT COMPUTER CAN HELP

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Why 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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>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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NECESSARY 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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MOLECULAR BIOLOGY KNOWELEDGE
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PROTEIN STRUCUTRE AND FUNCTION
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APPLICATIONS 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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APPLICATIONS OF BIOINFORMATICS
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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 experimental
research.
• 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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SPECIALIZED FIELDS
• Computational Biology
• Genomics
• Proteomics
• Bioprogramming
• Cheminformatics
• Structural Biology
• Systems Biology
• Pharmacogenomics

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MAJOR 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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ASSIGNMENT -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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Test-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:ANd9GcSg58MFhqEDknaHb3nHWmkP6mMgUbCjD7ASmqII4befeov
n566L9w
• 4.
http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/imag
es/central_dogma.gif
• 5. https://encrypted-tbn3.gstatic.com/images?
q=tbn:ANd9GcRx8BAquGrTstZrdTzPvvfn2ItAnPVGsjK03JfzMZF6SbpdasC
FAw
• 6.https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcRc-CJZHa1e-
8Xj78HMvWR-FNzw0KF4tEHrmH8clOcCzlOeYT3i
• 7.
http://upload.wikimedia.org/wikipedia/commons/e/e6/Spombe_Pop2p_protei
n_structure_rainbow.png
• 8. https://encrypted-tbn1.gstatic.com/images?
q=tbn:ANd9GcSHmWGzX5jd6PvwdiaYdxnGcCKOXjmxBmoz_YiE7L1xLNv
zAkQvITmdSrRy
• 9. & 10.Book: Basic Bioinformatics by S.Ignacimuthu, s.j.