| Bioinformatics |
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PLANT BASED BIOINFORMATICS
– DEVELOPMENT OF BIODIVERSITY (PLANT GENETIC) RESOURCE
DATABASES AND NETWORKS |
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| Group Leader |
Dr. SUDERSHAN KUMAR,
SCI 'EI' |
Phone
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Work
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+91(0522) 2205831
Ext.209
(Direct) 2204026/25 |
| Home |
+91(0522) 2208119 |
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| Introduction |
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| The term bioinformatics is used to encompass almost
all computer applications in biological sciences.
It was originally coined in the mid-1980s for the analysis
of biological sequence data. It is essentially a fusion of various
facets of biological science (functional, structural and technological)
with mathematics, computer science and information technology.
The history of computing in biology goes back to the 1920s
when scientist were already thinking of establishing biological
laws solely from data analysis by induction. However, only the
development of powerful computers and the availability of experimental
data that can be readily treated by computation launched bioinformatics
as an independent field.
Bioinformatics is generally defined as implication of computer
science into the biological science. There are several definitions
for the word bioinformatics, some of which are:
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- Bioinformatics is the use of computers in solving information
problems in the life sciences, mainly; it involves the creation
of extensive electronic databases on genomes, protein sequences,
etc. Secondarily, it involves techniques such as the three-dimensional
modeling of biomolecules and biologic systems.
- Bioinformatics is an integration of mathematical, statistical
and computer methods to analyze biological, biochemical and
biophysical data.
- Bioinformatics is the science of developing computer databases
and algorithms for the purpose of speeding up and enhancing
biological research.
- Bioinformatics can be defined as the storage, manipulation
and analysis of biological information via computer science.
Bioinformatics is an essential infrastructure underpinning
biological research.
- Bioinformatics is the application of computer technology
to the management of biological information. Specifically,
it is the science of developing computer databases and algorithms
to facilitate and expedite biological research.
- Bioinformatics is the study of the inherent structure of
biological information and biological systems. It brings together
the avalanche of systematic biological data (e.g. genomes)
with the analytic theory and practical tools of computer science
and mathematics.
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| Divisions of Bioinformatics |
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Bioinformatics is a multi disciplinary subject
and is very important for the growth of biosciences, biotechnology,
and the economic prosperity of nations. The following are the
well-identified subdivisions of Bioinformatics:
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- Molecular Bioinformatics,
- Cellular and sub-cellular Bioinformatics including epigenetics,
and neuro Bioinformatics,
- Orgasmic and community Bioinformatics,
- Medical Bioinformatics including metabolic pathways,
- Species Diversity Bioinformatics including behaviour, evolution
and the effect of pollutants on higher as well lower species.
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| Molecular Bioinformatics is the advanced branch
of Bioinformatics, but other two branches are lesser-developed
branch. Cellular and sub cellular Bioinformatics focuses on the
understanding of the functioning living cell. Orgasmic and community
Bioinformatics deals with Biodiversity and conservation aspects. |
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| Needs of Bioinformatics in Biology |
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| Computers play tremendous role in all the fields,
Contribution in biology is in the form of Database, Tools for
analyzing and predicting the Protein/ Nucleotide sequence, and
Generating/ Visualizing the 3-D structures of Biomolecules, etc.
Main aspiration of Bioinformatics is: |
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- To solve the bulk amount of data generated by Biological
Experiments.
- To make biological data available to scientists.
- To make biological data available in computer-readable
form.
- To refine the data according to requirement.
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| The following table lists the important and famously
known tools of Bioinformatics |
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A few notable Bioinformatics
tools |
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Tool Name |
Description |
| Blast 2.0 (Basic
Local Alignment Search Tool) |
Provide a method for rapid searching
of nucleotide and protein databases. BLAST algorithm
detects local as well as global alignments.
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| GeneBank (Genetic
sequence database) |
It is one of the fastest growing repositories
of known genetic sequences. GeneBank files contain
information like accession numbers and gene
names, phylogenetic classification and references
to published literature.
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| EMBL (European
Molecular Biology Laboratory) |
The EMBL nucleotide sequence database
is comprehensive database of DNA and RNA sequences
collected from the scientific literature and patent
application and directly submitted from researchers and
sequencing group.
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| PDB (Protein Data
Bank) |
The X-ray crystallography protein data
bank, compiled at Brookhaven National Laboratory.
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| PIR-PSD (Protein
Information Resource–Protein Sequence
Database) |
It is the most comprehensive and expertly
annotated protein sequence database.
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| Swiss Prot |
This is a protein sequence database
that provides a high level of integration with
other database and also has very low level of redundancy.
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| PROSITE |
Prosite is a database of protein family
and domains. It a method of determining what
is the function of uncharacterized proteins translated
from genomic or cDNA sequences.
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| Plant Based Bioinformatics |
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| Plants based Bioinformatics may be defined as the
area/ branch of information technology that deals with all aspects
of biological systems and associated scientific and technological
information/ data including the traditional knowledge systems-'data
mining' with the aim of conservation, sustainable utilization
that converts bioresources into economic wealth.
It involves information pertaining to biological resources,
inventory documentation, acquisition, processing, storage, distribution,
analysis and interpretation, that combines the tools and techniques
of mathematics, computer science, and biology with the aim of
understanding the biological significance of a variety of data.
Protein analysis, cell metabolism, biodiversity, biotechnology,
downstream processing in chemical engineering, genetic engineering,
and vaccine designs and diagnostic kits, etc., are other important
areas in which Bioinformatics constitute an integral component.
Plant Bioinformatics deals with plants and it’s allied
fields like molecular, cellular, systematic biology and so on.
Bioinformatics tools make the plant based research easier and
efficient by getting clue from existing experiments.
Plant databases are made for different purposes for organizing
the information in a meaningful manner. Generalized database
provides information about all plants in general but specialized
database are mainly for a particular plant or plant family.
Some well known plant databases are listed in the Table below.
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A few well known Plant databases |
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Plant
Database Name |
Description |
| Arabidopsis Genome
Resource (AGR) |
This provides information for identifying
gene function and crop plant orthologues
of Arabidopsis genes.
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| AraClean |
The database is a corrected and redundancy
reduced database of Arabidopsis thaliana sequences
extracted from GenBank.
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| Pisum sativum Genetics |
PSG contains Information on Pea genetics.
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| Maize Genome Database |
MaizeDB project is a part of the National
Agricultural Library's Plant Genome Research
Program. This provides access to Maize-related information
in a variety of formats.
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| Soybean Metabolic Database |
SoyBase a soybean genetic database,
contains reaction and pathway descriptions and
diagrams for a number of basic metabolic pathways.
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Mendel -
Plant Gene Nomenclature Database |
Mendel provides a common nomenclature
for sequenced genes, based on gene families,
for all photosynthetic organisms, the organelle
genomes of both photosynthetic and non-photosynthetic
organisms (fungi, algae, and protozoa) and plant viruses.
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| Dendrome |
The database is a collection of specialized
forest tree genome databases, which are being
developed by the Institute of Forest Genetics.
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| The Plant Chromatin Database |
PC database provides information on
Functional Genomics of Plant Chromatin Genes.
Presently holds Arabidopsis, maize and rice species,
as well as Chlamydomonas reinhardtii.
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| International Legume database
Information Service (ILDIS) |
This is a specialized database created
for species diversity database on Leguminosae.
The premier purpose of ILDIS is to provide a global
species diversity information service over 19000 taxa of
the plant family Leguminosae.
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| World Scenario |
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| Bioinformatics is rapidly growing throughout the
world. Several bioinformatics networks have been established like
International Center for Cooperation in Bioinformatics Network
(ICCBnet) to exchange the information and products. Molecular
biology servers are available from esteemed research institute
like National Center for Biotechnology information and European
Molecular Biology Laboratory (NCBI). Some important developmental
phases are: |
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| 1970 The Protein Data Bank (PDB)
was established.
1986 SWISS-PROT is a protein sequence database,
started by Amos Bairoch in the Department of Medical
Biochemistry at the University of Geneva.
1994 The SCOP (Structural Classification of
Proteins) database was started by Alexey Murzin at Lab of Molecular
Biology, MRC, Cambridge, UK. Its purpose is to classify protein
3D structures in a hierarchical
scheme of Structural classes.
1995 The CATH database (Class, Architecture,
Topology, Homologous superfamily) is a hierarchical classification
of protein domain structures. It was started by Christine Orengo
in Janet Thornton's lab
(University College London)
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| Indian scenario |
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| Indian government has taken a range of steps for
the growth of Bioinformatics. The major activity includes establishment
of Biotechnology Information System Network (BTIS net). It is
a National Bioinformatics Network in operation since 1987. The
Biotechnology Information System (BTIS) programme of the Department
of Biotechnology was launched during the 7th Five Year Plan to
harness the scientific knowledge in various inter-disciplinary
areas of biotechnology.
The programme comprises a distributed database & network,
namely, BTISnet. The network mainly consists of sixty-one bioinformatics
centers spread all over the country. It has established a link
among the scientist and organization involved in research and
development activities in biotechnology.
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