Online Counseling Resource
YCMOU ELearning Drive…
School of Architecture, Science and Technology
Yashwantrao Chavan Maharashtra
Open University, Nashik – 422222, India
OC_SEP –SBI081– CP1_05
Introduction
Programmes and Courses
 SEP-SBI081– U1-CP1
School of Science and Technology, Online Counseling Resource…
Credits
 Academic Inputs by
Sonali Alkari
Faculty YCMOU Nagpur Centre,
Faculty LAD college P.G. D of Biotechnology
Research officer Ankur Seeds Pvt Ltd
[email protected]
[email protected]
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School of Science and Technology, Online Counseling Resource…
How to Use This Resource

Counselor at each study center should use this presentation to deliver
lecture of 40-60 minutes during Face-To-Face counseling.

Discussion about students difficulties or tutorial with assignments should
follow the lecture for about 40-60 minutes.

Handouts (with 6 slides on each A4 size page) of this presentation should
be provided to each student.

Each student should discuss on the discussion forum all the terms which
could not be understood. This will improve his writing skills and enhance
knowledge level about topics, which shall be immensely useful for end
exam.

Appear several times, for all the Self-Tests, available for this course.

Student can use handouts for last minutes preparation just before end
exam.
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Learning Objectives
 After studying this module, you should be
able to browse Genomic databases for:
 Plant,
 Microbial,
 Parasite and
 Viral genomes
© 2007, YCMOU. All Rights Reserved.
School of Science and Technology, Online Counseling Resource…
Plant Genome-1
 Plants are organisms belonging to the kingdom




Planate.
They include familiar organisms such as trees,
herbs, bushes, grasses, vines, fern, mosses and
green algae.
About 350,000 species of plants, defined as seed
plants, bryophytes, ferns and fern allies, are
estimated to exist currently.
Green plants, sometimes called metaphytes or
viridiplantae, obtain most of their energy from
sunlight via a process called photosythesis.
The whole world is dependent plant for nutrition
and other resources, so it is necessary to study
plants in details for their improvement.
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Plant Genome-2
 Eukaryotic genomes are much more complex than
prokaryotic genomes. Plant genomes are more
complex than other eukaryotic genomes.
 Prior to the development of recombinant DNA
technology
genomes,
were
analysed
by
reassociation kinetics techniques.
 Reassociation kinetic experiments are performed by
melting DNA and allowing it to reanneal upon itself
or with another population of either DNA or RNA
molecules.
 The kinetics of the reassociation provide data that
can be used to analyze the overall structure,
evolution and expression of genomes.
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Plant Genome-3
 The MOsDB is a resource for publicly available
sequences of the rice (Oryza sativa L.) genome.
 Rice is an experimental model for the cereal crops
research and an agriculturally important plant,
providing food for more than half of the world
population.
 The estimated rice genome size is about 430 Mb,
which is the smallest among all the cereal crops and
about one seventh of human and 3.5 times of
Arapdopsis genomes.
 The goal at MOsDB is to provide all available data
about rice genes and genomics, including (in the
future) mutant information and expression profiles.
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Plant Genome-4
 The MOsDB database includes current (updated on
daily basis) published sequences and gene annotation
information of two Oryza sativa subspecies: japonica
and indica..
 The International Rice Genome Sequencing Project
deploys a chromosome by chromosome, clone by
clone approach, and deposits BAC/PAC-sized contigs
to the public databases.
 Monsanto and Syngenta, two US-operating companies,
have also announced the establishment of working
drafts of the rice genome at different coverage in April
of 2000 and February of 2001, respectively
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Plant Genome-5
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Plant Genome-6
 The genome sequence of O.s. spp indica was
obtained by a "whole genome shotgun".
 The project was initiated in May, 2000 at
Beijing Genomics Institute and the working
draft was done in Oct. 2001.
 The release covers the draft sequence assembly
of the rice genome from 93-11, a cultivar of
domesticated rice subspecies (indica), the
major rice subspecies cultivated in China and
many other Asian-pacific regions.
 Functional
coverage
of
the
assembled
sequence, based on STSs, ESTs, and full-length
cDNAs, is estimated to be 92%.
© 2007, YCMOU. All Rights Reserved.
School of Science and Technology, Online Counseling Resource…
Microbial Genome Projects
 Microbes are the organisms which are not visual
to naked eye and studied with help of
microscope.
 Microbial
genome projects offers a timely
summary of the principles, approaches, and
applications.
 It presents a comprehensive review of
microbial
functional
genomics,
covering
microbial
diversity,
microbial
genome
sequencing, genomic technologies, genomewide functional analysis, applied functional
genomics, and future directions.
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Microbial Genome-1
 Encyclopedia of Escherichia coli K-12 Genes
and Metabolism
 EcoCyc is a scientific database for the
bacterium Escherichia coli K-12 MG1655.
 The EcoCyc project performs literature-based
curation of the entire genome, and of
transcriptional regulation, transporters, and
metabolic pathways.
 "Multidimensional
annotation
of
the
Escherichia coli K-12 Genome," Nucleic Acids
Research.
 The EcoCyc web site is updated quarterly.
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Microbial Genome-2
 E. coli Wiki it integrates a number of
existing E. coli databases, and it will capture
E. coli functional genomics data and
sequence data for non-pathogenic E. coli
strains.
 Our vision is for these two resources to form
a seamless information infrastructure for E.
coli.
Both
projects
are
funded
by
NIH/NIGMS.
© 2007, YCMOU. All Rights Reserved.
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Parasite Genome Projects-1
 The parasites are the organisms which can not
synthesis their own food, they are dependent on
other organisms for food.
 Their association with host may be benefical to host
or may be harmful, hence their study is very
important.
 The parasites genome projects revealed important
metabolic pathways which can be targeted to develop
antiparasite drugs and antigens for potentialvaccines.
 However, many other fruitful results can be obtained
using comparative genomics in
this field, for
example regulation of transcription is still quite
unknown in these organisms.
© 2007, YCMOU. All Rights Reserved.
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Parasite Genome Projects-2
 The Trypanosoma cruzi Genome Project
 Trypanosoma brucei Genome Project
 Trypanosoma brucei genome sequencing
at Sanger
 Trypanosoma brucei genome sequencing
at TIGR
 LGN- Leishmania Genome Network
 Leishmania Genome sequencing in Seattle
 Leishmania Genome sequencing at Sanger
Leishmania network.
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Parasite Genome Projects-3
 Plasmodium Gene Identification program
P.falciparum.
 Plasmodium falciparum Gene Sequence Tag
project.
 Plasmodium falciparum Genome Sequencing
(Sanger Centre)
 Malaria Network WWW site (Australia)
 Malaria Genome site (Australia)
 Malaria-WHO, Malaria database (from WHO)
Malaria Antigen Database
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Parasite Genome Projects-4
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Parasite Genome Projects-5
 PlasmoDB.org hosts genomic and proteomic
data (and more) for different species of the
parasitic eukaryote Plasmodium, the cause of
Malaria.
 It brings together data provided by numerous
laboratories worldwide, and adds its own data
analysis.
 Publications relying on PlasmoDB should
acknowledge the database developers and the
scientists who have made their data available.
 PlasmoDB is part of an NIH/NIAID funded
Bioinformatics Resource centre to
provide
Apicomplexan
Database
Resources.
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Parasite Genome Projects-6
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Parasite Genome Projects-7
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Viral Genome Project
 A virus (from the latin virus meaning "toxin" or
"poison"), is a sub-microscopic
infectious
agent that is unable to grow or reproduce
outside a host cell.
 All living things are susceptible to viral
infections ... plants, animals, or bacteria can all
be infected by a virus specific for that type of
organism.
 The difficulty in developing antiviral therapies
stems from the large number of variant viruses
that can cause the same disease, as well as the
inability of drugs to disable a virus without
disabling healthy cells
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Viral Genomes-1
 VIDA contains a complete collection of
homologous protein families derived from
open reading frames from complete and
partial virus genomes.
 For each family you can get an alignment of
the conserved regions, functional and
taxonomy information, and links to DNA
sequences and structures.
 "VirOligo"
is
derived
from
Virus
Oligonucleotide.
The
VirOligo
database
collects virus-specific oligonucleotides for
virus detection from published literature.
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Viral Genomes-2
Homologous protein family search
Search by:
 homologous protein family number
 virus name (choose from list)
 protein function (keyword/functional
class)
 GenBank protein number
 free text
 Search by sequence similarity
 Search profiles
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Viral Genomes-3
Sample List of Viruses
 SARS Coronavirus
 Foot-and-Mouth disease virus
 Variola (Small pox) virus
 Influenza A virus
 Bovine herpesvirus
 Bovine viral diarrhea virus
 Bovine respiratory syncytial viru
 Alcelaphine herpesvirus
 Bovine adenovirus
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Viral Genomes-4
Data available on homologous protein families
from the following virus families:
 Arteriviridae
 Coronaviridae
 Herpesviridae
 Papillomaviridae
 Poxviridae
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Viral Genomes-5
 Links to complete genome sequences :
Arteriviridae , Coronaviridae , Herpesviridae ,
Poxviridae.
 Analyse virus sequences with Virus Genome
Annotator .
 Gene Ontology herpes simplex virus 1
GO_HSV-1.
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What You Learn-1…
 Plants are source of energy for whole world, so it is
very important to study plant genome in details.
 The genome databases creation is in progress for
maize, rice, tomato .
 The model organisms for plant genome is Arabidopsis
thaliana .
 The parasite and microbes are model organisms for
one or the other purpose, so their study and genome
database creation will be helpful in understand
diseases and developing drugs.
 Viruses are very important , as they are on the
boundary line of living and non-living organisms.
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What You Learn-2…
 Viruses are utilize in biotechnology work as vector
and for other some many purposes, so virus
genome database creation will be a mile stone.
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Critical Thinking Questions
1. Write a short note on plant
project and its outcome.
genome
2. Write a short note on parasite and
microbial genome project and its
outcome.
3. Write a short note on virus genome
project and its outcome.
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Hints For Critical Thinking Question
1. What are plants, their
outcome of the project.
importance
2. What are parasites and microbes,
importance and outcome of the project.
and
their
3. What is virus, its importance and outcome of
the project.
© 2007, YCMOU. All Rights Reserved.
31
School of Science and Technology, Online Counseling Resource…
Study Tips:1
 Book1
 Title: Principles of Genome Analysis And
Genomics
 Author: Primrose, S.B. & Twyman, R.M.
 Publisher: Blackwell Publishing Company.
 Book2
 Title: Bioinformatics: A Practical Guide to the
Analysis of Genes and Proteins
 Author: Andreqas D. Baxevanis, B. F. Francis
Ouellette
 Publisher: John Wiley and Sons, New York
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Study Tips:2
 Book3
 Title: Bioinformatics Sequence and Genome
Analysis
 Author:David W. Mount.
 Publisher: Cold Spring Harborlaboratory
Press.
 Book4
 Title: Bionformatics Concepts, Skills and
Application
 Author: Rastogi, S.C., Mendiratta N, Rastogi ,
 Publisher: CBS Publishers & Distributors
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Study Tips
www.en.wikipedia.org
Microsoft Encarta Encyclopedia
http://en.wikipedia.org/wiki/
Wikipedia the free encyclopedia
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End of the Presentation
Thank You
© 2007, YCMOU. All Rights Reserved.