SlideShare a Scribd company logo
Genome projects and the development of our current
information library
 Name: Zarlish Attique
 Roll no: 187104
 BS: Bioinformatics
 Semester: 5th
 Subject: Genomics
 Teacher: Muhammad Rizwan
 Date: 12,January,2020
Government Post Graduate College Mandian Abbottabad
Power point slides created by Zarlish Attique
Table of Contents
• Genome projects
• Different types of genome projects
• Genome projects for five kingdom classification
• Methods use for genome projects
• Current information library and conclusion
Genome Projects
Scientific endeavors ultimately aim to determine the
complete genome sequence of an organism and to
annotate protein-coding genes and other important
genome-encoded features.
1. Genome Assembly: the process of taking a large
number of short DNA sequences and putting them
back together to create a representation of the
original chromosomes from which the DNA
originated.
2. Genome annotation: the process of identifying
attaching biological information to sequences , and
particularly in identifying the locations of genes and
determining what those genes do.
Figure: Represents different important stages
and involvements in the genome projects.
Genome Projects and development of our current information
library
3
Some genome projects
o Genomic Science Program: microbes and plants at
the molecular, cellular, and community levels. a
predictive understanding of how living systems operate.
https://genomicscience.energy.gov/
o ENCODE: ENCyclopedia of DNA Elements: In
September 2003, to carry out a project to identify all
functional elements in the human genome sequence.
o The 100,000 Genomes Project Wellcome Trust
Sanger Institute in Hinxton; the Beijing Genomics
Institute Shenzhen; and the US NIH National Human
Genome Research Institute.
https://www.internationalgenome.org/data
Genome Projects and development of our current information
library
4
Some genome projects
o Roadmap Epigenomics Project: Producing a public
resource of human epigenomic data to catalyze basic biology
and disease-oriented research and to map DNA methylation,
histone modifications, chromatin accessibility and small RNA
transcripts.
http://www.roadmapepigenomics.org/
o Genographic Project: Led by National Geographic and IBM:
technologies to analyze historical patterns in DNA from
participants around the world to better understand our human
genetic roots.
https://www.nationalgeographic.com/sorry/genographic
o Knockout Mouse Phenotyping Program (KOMP2):
Leading the way as part of the International Mouse
Phenotyping Consortium (IMPC) in understanding the aging
process and diseases that occur later in life.
Genome Projects and development of our current information
library
5
Some genome projects
o International HapMap Project: a haplotype map of the
human genome: to find genes affecting health, disease, and
responses to drugs and environmental factors.
http://www.hapmap.org/
o Microbial Genome Project: U.S. Department of Energy
(DOE) led the Microbial Genome Project from 1994-
2005.:finding alternative sources of energy, understanding
biological carbon cycling.
o Environmental Genome Project: complex inter-
relationship between multiple genetic and environmental
factors. Goal of the EGP is to characterize how specific
human genetic variations, or polymorphisms, contribute to
environmentally induced disease susceptibility.
https://www.niehs.nih.gov/
Genome Projects and development of our current information
library
6
Some genome projects
o Cancer Genome Anatomy Project: to determine the gene
expression profiles of normal, precancer, and cancer cells,
leading eventually to improved detection, diagnosis, and
treatment for the patient.
https://cgap.nci.nih.gov/
o Chimpanzee genome Project: by comparing the genomes
of humans and other apes, to better understand what makes
humans distinct from other species from a genetic perspective,
published in Nature on September 1, 2005, there are
differences between human and chimpanzee genes.
o 100K Pathogen Genome Project: launched in July 2012,
infectious microorganisms to create a database of bacterial
genome sequences for use in public health, outbreak detection,
and bacterial pathogen detection.
https://www.internationalgenome.org/data
Genome Projects and development of our current information
library
7
Species Strain Base Pairs Genes
Akkermansia muciniphila ATCC BAA-835 2,664,102 2,176
Akkermansia muciniphila Urmite 2,664,714 2,192
Chlamydia muridarum Nigg 1,072,950 904
Chlamydia trachomatis AHAR13 1,044,459 911
Chlamydia trachomatis DUW 1,042,519 894
Chlamydophila abortus S26-3 1,144,377 961
MONERA
Following are the sequenced genomes of monerans.
Genome Projects and development of our current information
library
8
Protists
Following are the six earliest sequenced genomes of protists.
Organism Genome size Organization Year of
completion
Guillardia theta 0.551 Mb Canadian Institute of Advanced
Research, Philipps-University Marburg and
the University of British Columbia
2001
Plasmodium falciparum
Clone:3D7
22.9 Mb Malaria Genome Project Consortium 2002
Plasmodium yoelii yoelii
Strain:17XNL
23.1 Mb TIGR and NMRC 2002
Cryptosporidium hominis
Strain:TU502
10.4 Mb Virginia Commonwealth University 2004
Cryptosporidium parvum
C- or genotype 2 isolate
16.5 Mb UCSF and University of Minnesota 2004
Thalassiosira pseudonana
Strain:CCMP 1335
34.5 Mb Joint Genome Institute and the University of
Washington
2004
Genome Projects and development of our current information
library
9
Plants
Following are the five earliest sequenced genomes of plants.
Organism Genome size Organization Year of
completion
Arabidopsis thaliana
Ecotype:Columbia
135 Mb Arabidopsis Genome Initiative 2000
Cyanidioschyzon merolae
Strain:10D
16.5 Mb University of Tokyo, Rikkyo University, Saitama
University and Kumamoto University
2004
Oryza sativa
ssp indica
420 Mb Beijing Genomics Institute, Zhejiang University
and the Chinese Academy of Sciences
2002
Ostreococcus tauri 12.6 Mb Laboratoire Arago 2006
Populus trichocarpa 550 Mb The International Poplar Genome Consortium 2006
Genome Projects and development of our current information
library
10
Fungi
Organism Genome
size
Organization Year of
completion
Saccharomyces cerevisiae
Strain:S288C
12.1 Mb International Collaboration for the Yeast Genome
Sequencing
1996
Encephalitozoon cuniculi 2.9 Mb Genoscope and Université Blaise Pascal 2001
Schizosaccharomyces pombe
Strain:972h-
14 Mb Sanger Institute and Cold Spring Harbor Laboratory 2002
Neurospora crassa 40 Mb Broad Institute Oregon Health and science
university, University of Kentucky, and the University of
Kansas
2003
Phanerochaete chrysosporium
Strain:RP78 Imagine!
30 Mb Joint Genome Institute 2004
Following are the five earliest sequenced genomes of fungi.
Genome Projects and development of our current information
library
11
Animals
Following are the five earliest sequenced genomes of animals.
Organism Genome
size
Number of
genes
predicted
Organization Year of completion
Caenorhabditis elegans
Strain:Bristol N2
100 Mb 19,000 Washington University and the Sanger
Institute
199
Drosophila melanogaster 165 Mb 13,600 Celera, UC Berkeley, Baylor College of
Medicine, European DGP
2000
Anopheles gambiae
Strain: PEST
278 Mb 13,683 Celera Genomics and Genoscope 2002
Takifugu rubripes 390 Mb 22–29,000 International Fugu Genome
Consortium
2002
Homo sapiens 3.2 Gb 18,826 (CCDS
consortium)
Human Genome Project
Consortium and Celera Genomics
Draft 2001
Complete 2006
Genome Projects and development of our current information
library
12
Viruses
Organism Genome size
(base pairs)
Note
Porcine circovirus type 1 1,759 1.8kb Smallest viruses replicating
autonomously in eukaryotic cells.
Bacteriophage MS2 3,569 3.5kb First sequenced RNA-genome
SV40 5,224 5.2kb
Phage Φ-X174 5,386 5.4kb First sequenced DNA-genome
HIV 9,749 9.7kb
Phage λ 48,502 48.5kb Often used as a vector for the
cloning of recombinant DNA.
Following are the sequenced genomes of viruses.
Genome Projects and development of our current information
library
13
High-throughput
sequencing
Genome Projects and development of our current information
library
14
High-throughput sequencing
Genome Projects and development of our current information
library
15
High-throughput sequencing
Genome Projects and development of our current information
library
16
High-throughput sequencing
Genome Projects and development of our current information
library
17
High-throughput sequencing
Genome Projects and development of our current information
library
18
De novo sequencing
Genome Projects and development of our current information
library
19
Resequencing
Genome Projects and development of our current information library
20
21
Exome sequencing
21
Genome Annotation
• http://www.repeatmasker.org/
• Types of repeats found in the genome, Regulatory elements, Homologues in other species,ORF etc.
Genome Projects and development of our current information library 22
Name Can be Used For
GeneMark Archaea, Metagenomes ,Eukaryotes,Viruses, Phages, Plasmids, EST and cDNA
GeneHacker Microbial genomes
GeneWalker Human
HMMgene (v. 1.1) vertebrate and C. elegans
Chemgenome2.0 Prokaryotes
Softberry Server Bacteria ,Viruses and eukaryotes
Gene ID Animal, Human, Plants fungus, Protists
GenScan Vertebrates, Arabidopsis, Maize
Phytophthora
annotation report
23
Genome
Projects
and
development
of
our
current
information
library
Current information library
1. The past few years have seen truly astounding progress in the development of high-throughput
sequencing techniques.
2. Initial determination of a draft of the human genome took ten years, at an estimated cost of $US 3
´ 109.
3. Now instruments exist that can produce 250 Gb per week.
4. Currently in Shenzhen – has 128 such instruments. Each can produce 25 ´ 109 bp per day! This
corresponds to one human genome at over 8X coverage. Running at full capacity, these resources
could produce 10 000 human genomes per year.
5. Moreover, there is no reason to think that the technical progress will not continue to accelerate.
6. Two aspects of a large-scale sequencing project.
7. One is the generation of the raw data. Most methods sequence long DNA molecules by
fragmenting them, and partially sequencing the pieces.
8. Both generation of raw data, and assembly, depend crucially on effective and efficient computer
programs.
References
1. https://www.sciencedirect.com/topics/neuroscience/genome-project
2. https://www.nature.com/articles/nbt1000_1049
3. https://benthamscience.com/journals/current-bioinformatics/library-recommendations/
4. https://www.studocu.com/en-us/document/california-institute-of-technology/human-
genetics-and-genomics/other/introduction-to-genomics-second-edition-arthur-m-
lesk/1587322/view
5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1525323/
Any Question: Feel free to ask!
Genome Projects and development of our current information
library
25

More Related Content

What's hot

Yeast genome project
Yeast genome projectYeast genome project
Yeast genome project
Nazish_Nehal
 
Genomics seminar copy
Genomics seminar   copyGenomics seminar   copy
Genomics seminar copy
manjunatha s s
 
L14 human genome
L14 human genomeL14 human genome
L14 human genomeMUBOSScz
 
Yeast Genome
Yeast Genome Yeast Genome
Plant genome project (COBAM, UOP, Peshawar)
Plant genome project (COBAM, UOP, Peshawar)Plant genome project (COBAM, UOP, Peshawar)
Plant genome project (COBAM, UOP, Peshawar)Qaisar Khan
 
THE human genome
THE human genomeTHE human genome
THE human genome
rokanuzzaman moschus
 
Human genome project
Human genome projectHuman genome project
Human genome project
Shital Pal
 
Cracking the code of life
Cracking the code of lifeCracking the code of life
Cracking the code of lifegmtrainor3
 
Rice genome india"s role
Rice genome india"s  role Rice genome india"s  role
Rice genome india"s role
deepakrai26
 
Whole genome sequencing of bacteria & analysis
Whole genome sequencing of bacteria & analysisWhole genome sequencing of bacteria & analysis
Whole genome sequencing of bacteria & analysisdrelamuruganvet
 
Evolution of DNA Sequencing by Jonathan Eisen
Evolution of DNA Sequencing by Jonathan EisenEvolution of DNA Sequencing by Jonathan Eisen
Evolution of DNA Sequencing by Jonathan Eisen
Jonathan Eisen
 
When is a genome finished?
When is a genome finished? When is a genome finished?
When is a genome finished?
Keith Bradnam
 
Overview on arabidopsis and rice genome
Overview on arabidopsis and rice genomeOverview on arabidopsis and rice genome
Overview on arabidopsis and rice genome
Gopal Singh
 
Human Genome Project
Human Genome ProjectHuman Genome Project
Human Genome Project
Peyman Ghoraishizadeh
 
Genome sequencing in vegetable crops
Genome sequencing in vegetable cropsGenome sequencing in vegetable crops
Genome sequencing in vegetable crops
Bommesh
 
PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICS
PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICSPROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICS
PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICS
Lubna MRL
 
Genomics 101 jun 15 2012
Genomics 101 jun 15 2012Genomics 101 jun 15 2012
Genomics 101 jun 15 2012Genome Alberta
 
Human Genome Project
Human Genome ProjectHuman Genome Project
Human Genome Project
Sachin Rawat
 
Next Generation Sequencing and its Applications in Medical Research - Frances...
Next Generation Sequencing and its Applications in Medical Research - Frances...Next Generation Sequencing and its Applications in Medical Research - Frances...
Next Generation Sequencing and its Applications in Medical Research - Frances...
Sri Ambati
 

What's hot (20)

Yeast genome project
Yeast genome projectYeast genome project
Yeast genome project
 
Genomics seminar copy
Genomics seminar   copyGenomics seminar   copy
Genomics seminar copy
 
L14 human genome
L14 human genomeL14 human genome
L14 human genome
 
Yeast Genome
Yeast Genome Yeast Genome
Yeast Genome
 
Plant genome project (COBAM, UOP, Peshawar)
Plant genome project (COBAM, UOP, Peshawar)Plant genome project (COBAM, UOP, Peshawar)
Plant genome project (COBAM, UOP, Peshawar)
 
THE human genome
THE human genomeTHE human genome
THE human genome
 
Human genome project
Human genome projectHuman genome project
Human genome project
 
Cracking the code of life
Cracking the code of lifeCracking the code of life
Cracking the code of life
 
Rice genome india"s role
Rice genome india"s  role Rice genome india"s  role
Rice genome india"s role
 
Whole genome sequencing of bacteria & analysis
Whole genome sequencing of bacteria & analysisWhole genome sequencing of bacteria & analysis
Whole genome sequencing of bacteria & analysis
 
Evolution of DNA Sequencing by Jonathan Eisen
Evolution of DNA Sequencing by Jonathan EisenEvolution of DNA Sequencing by Jonathan Eisen
Evolution of DNA Sequencing by Jonathan Eisen
 
Embed Repro Test
Embed Repro TestEmbed Repro Test
Embed Repro Test
 
When is a genome finished?
When is a genome finished? When is a genome finished?
When is a genome finished?
 
Overview on arabidopsis and rice genome
Overview on arabidopsis and rice genomeOverview on arabidopsis and rice genome
Overview on arabidopsis and rice genome
 
Human Genome Project
Human Genome ProjectHuman Genome Project
Human Genome Project
 
Genome sequencing in vegetable crops
Genome sequencing in vegetable cropsGenome sequencing in vegetable crops
Genome sequencing in vegetable crops
 
PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICS
PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICSPROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICS
PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICS
 
Genomics 101 jun 15 2012
Genomics 101 jun 15 2012Genomics 101 jun 15 2012
Genomics 101 jun 15 2012
 
Human Genome Project
Human Genome ProjectHuman Genome Project
Human Genome Project
 
Next Generation Sequencing and its Applications in Medical Research - Frances...
Next Generation Sequencing and its Applications in Medical Research - Frances...Next Generation Sequencing and its Applications in Medical Research - Frances...
Next Generation Sequencing and its Applications in Medical Research - Frances...
 

Similar to Genome sequencing and the development of our current information library

The Emerging Global Community of Microbial Metagenomics Researchers
The Emerging Global Community of Microbial Metagenomics ResearchersThe Emerging Global Community of Microbial Metagenomics Researchers
The Emerging Global Community of Microbial Metagenomics Researchers
Larry Smarr
 
Comparative genomics and proteomics
Comparative genomics and proteomicsComparative genomics and proteomics
Comparative genomics and proteomicsNikhil Aggarwal
 
Web Apollo: Lessons learned from community-based biocuration efforts.
Web Apollo: Lessons learned from community-based biocuration efforts.Web Apollo: Lessons learned from community-based biocuration efforts.
Web Apollo: Lessons learned from community-based biocuration efforts.
Monica Munoz-Torres
 
Human genome project
Human genome projectHuman genome project
Human genome project
ruchibioinfo
 
Human genome project by kk sahu
Human genome project by kk sahuHuman genome project by kk sahu
Human genome project by kk sahu
KAUSHAL SAHU
 
Human genome project
Human genome projectHuman genome project
Human genome project
Dilip jaipal
 
Microbial Metagenomics Drives a New Cyberinfrastructure
Microbial Metagenomics Drives a New CyberinfrastructureMicrobial Metagenomics Drives a New Cyberinfrastructure
Microbial Metagenomics Drives a New Cyberinfrastructure
Larry Smarr
 
Bioinformatics
BioinformaticsBioinformatics
Bioinformatics
Vidya Kalaivani Rajkumar
 
PAPER 3.1 ~ HUMAN GENOME PROJECT
PAPER 3.1 ~  HUMAN GENOME PROJECTPAPER 3.1 ~  HUMAN GENOME PROJECT
PAPER 3.1 ~ HUMAN GENOME PROJECT
Nusrat Gulbarga
 
Genome Projects : Human, Rice,Wheat,E coli and Arabidopsis.
Genome Projects : Human, Rice,Wheat,E coli and Arabidopsis.Genome Projects : Human, Rice,Wheat,E coli and Arabidopsis.
Genome Projects : Human, Rice,Wheat,E coli and Arabidopsis.
Cherry
 
rheumatoid arthritis
rheumatoid arthritisrheumatoid arthritis
rheumatoid arthritis
Ankit Bhardwaj
 
An Introduction to Genomics
An Introduction to GenomicsAn Introduction to Genomics
An Introduction to Genomics
Dr NEETHU ASOKAN
 
Conservation Biotechnology: DNA and Tissue Bank, DNA Barcoding , DNA fingerpr...
Conservation Biotechnology: DNA and Tissue Bank, DNA Barcoding, DNA fingerpr...Conservation Biotechnology: DNA and Tissue Bank, DNA Barcoding, DNA fingerpr...
Conservation Biotechnology: DNA and Tissue Bank, DNA Barcoding , DNA fingerpr...
AnitaPoudel5
 
Human genome project
Human genome projectHuman genome project
Human genome project
sabahayat3
 
Human genome project (2) converted
Human genome project (2) convertedHuman genome project (2) converted
Human genome project (2) converted
GAnchal
 
Diversity Diversity Diversity Diversity ....
Diversity Diversity Diversity Diversity ....Diversity Diversity Diversity Diversity ....
Diversity Diversity Diversity Diversity ....
Jonathan Eisen
 
Bioinformatics group presentation
Bioinformatics group presentationBioinformatics group presentation
Bioinformatics group presentation
Naeem Ahmed
 
Bioinformatics group presentation
Bioinformatics group presentationBioinformatics group presentation
Bioinformatics group presentation
Naeem Ahmed
 
The human genome project was started in 1990 with the goal of sequencing and ...
The human genome project was started in 1990 with the goal of sequencing and ...The human genome project was started in 1990 with the goal of sequencing and ...
The human genome project was started in 1990 with the goal of sequencing and ...Rania Malik
 
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
Larry Smarr
 

Similar to Genome sequencing and the development of our current information library (20)

The Emerging Global Community of Microbial Metagenomics Researchers
The Emerging Global Community of Microbial Metagenomics ResearchersThe Emerging Global Community of Microbial Metagenomics Researchers
The Emerging Global Community of Microbial Metagenomics Researchers
 
Comparative genomics and proteomics
Comparative genomics and proteomicsComparative genomics and proteomics
Comparative genomics and proteomics
 
Web Apollo: Lessons learned from community-based biocuration efforts.
Web Apollo: Lessons learned from community-based biocuration efforts.Web Apollo: Lessons learned from community-based biocuration efforts.
Web Apollo: Lessons learned from community-based biocuration efforts.
 
Human genome project
Human genome projectHuman genome project
Human genome project
 
Human genome project by kk sahu
Human genome project by kk sahuHuman genome project by kk sahu
Human genome project by kk sahu
 
Human genome project
Human genome projectHuman genome project
Human genome project
 
Microbial Metagenomics Drives a New Cyberinfrastructure
Microbial Metagenomics Drives a New CyberinfrastructureMicrobial Metagenomics Drives a New Cyberinfrastructure
Microbial Metagenomics Drives a New Cyberinfrastructure
 
Bioinformatics
BioinformaticsBioinformatics
Bioinformatics
 
PAPER 3.1 ~ HUMAN GENOME PROJECT
PAPER 3.1 ~  HUMAN GENOME PROJECTPAPER 3.1 ~  HUMAN GENOME PROJECT
PAPER 3.1 ~ HUMAN GENOME PROJECT
 
Genome Projects : Human, Rice,Wheat,E coli and Arabidopsis.
Genome Projects : Human, Rice,Wheat,E coli and Arabidopsis.Genome Projects : Human, Rice,Wheat,E coli and Arabidopsis.
Genome Projects : Human, Rice,Wheat,E coli and Arabidopsis.
 
rheumatoid arthritis
rheumatoid arthritisrheumatoid arthritis
rheumatoid arthritis
 
An Introduction to Genomics
An Introduction to GenomicsAn Introduction to Genomics
An Introduction to Genomics
 
Conservation Biotechnology: DNA and Tissue Bank, DNA Barcoding , DNA fingerpr...
Conservation Biotechnology: DNA and Tissue Bank, DNA Barcoding, DNA fingerpr...Conservation Biotechnology: DNA and Tissue Bank, DNA Barcoding, DNA fingerpr...
Conservation Biotechnology: DNA and Tissue Bank, DNA Barcoding , DNA fingerpr...
 
Human genome project
Human genome projectHuman genome project
Human genome project
 
Human genome project (2) converted
Human genome project (2) convertedHuman genome project (2) converted
Human genome project (2) converted
 
Diversity Diversity Diversity Diversity ....
Diversity Diversity Diversity Diversity ....Diversity Diversity Diversity Diversity ....
Diversity Diversity Diversity Diversity ....
 
Bioinformatics group presentation
Bioinformatics group presentationBioinformatics group presentation
Bioinformatics group presentation
 
Bioinformatics group presentation
Bioinformatics group presentationBioinformatics group presentation
Bioinformatics group presentation
 
The human genome project was started in 1990 with the goal of sequencing and ...
The human genome project was started in 1990 with the goal of sequencing and ...The human genome project was started in 1990 with the goal of sequencing and ...
The human genome project was started in 1990 with the goal of sequencing and ...
 
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
 

More from ZarlishAttique1

Automated and manual Primer designing and its validation using Bioinformatics...
Automated and manual Primer designing and its validation using Bioinformatics...Automated and manual Primer designing and its validation using Bioinformatics...
Automated and manual Primer designing and its validation using Bioinformatics...
ZarlishAttique1
 
Phylogenetic tree construction using bioinformatics tools Zarlish attique 187104
Phylogenetic tree construction using bioinformatics tools Zarlish attique 187104Phylogenetic tree construction using bioinformatics tools Zarlish attique 187104
Phylogenetic tree construction using bioinformatics tools Zarlish attique 187104
ZarlishAttique1
 
DBMS Helping material
DBMS Helping materialDBMS Helping material
DBMS Helping material
ZarlishAttique1
 
QSAR quantitative structure activity relationship
QSAR quantitative structure activity relationship QSAR quantitative structure activity relationship
QSAR quantitative structure activity relationship
ZarlishAttique1
 
Zarlish attique 187104 project assignment modeller
Zarlish attique 187104 project assignment modellerZarlish attique 187104 project assignment modeller
Zarlish attique 187104 project assignment modeller
ZarlishAttique1
 
Receptor Effector coupling by G-Proteins Zarlish attique 187104
Receptor Effector coupling by G-Proteins Zarlish attique 187104 Receptor Effector coupling by G-Proteins Zarlish attique 187104
Receptor Effector coupling by G-Proteins Zarlish attique 187104
ZarlishAttique1
 
Computational phylogenetics theoretical concepts, methods with practical on C...
Computational phylogenetics theoretical concepts, methods with practical on C...Computational phylogenetics theoretical concepts, methods with practical on C...
Computational phylogenetics theoretical concepts, methods with practical on C...
ZarlishAttique1
 

More from ZarlishAttique1 (7)

Automated and manual Primer designing and its validation using Bioinformatics...
Automated and manual Primer designing and its validation using Bioinformatics...Automated and manual Primer designing and its validation using Bioinformatics...
Automated and manual Primer designing and its validation using Bioinformatics...
 
Phylogenetic tree construction using bioinformatics tools Zarlish attique 187104
Phylogenetic tree construction using bioinformatics tools Zarlish attique 187104Phylogenetic tree construction using bioinformatics tools Zarlish attique 187104
Phylogenetic tree construction using bioinformatics tools Zarlish attique 187104
 
DBMS Helping material
DBMS Helping materialDBMS Helping material
DBMS Helping material
 
QSAR quantitative structure activity relationship
QSAR quantitative structure activity relationship QSAR quantitative structure activity relationship
QSAR quantitative structure activity relationship
 
Zarlish attique 187104 project assignment modeller
Zarlish attique 187104 project assignment modellerZarlish attique 187104 project assignment modeller
Zarlish attique 187104 project assignment modeller
 
Receptor Effector coupling by G-Proteins Zarlish attique 187104
Receptor Effector coupling by G-Proteins Zarlish attique 187104 Receptor Effector coupling by G-Proteins Zarlish attique 187104
Receptor Effector coupling by G-Proteins Zarlish attique 187104
 
Computational phylogenetics theoretical concepts, methods with practical on C...
Computational phylogenetics theoretical concepts, methods with practical on C...Computational phylogenetics theoretical concepts, methods with practical on C...
Computational phylogenetics theoretical concepts, methods with practical on C...
 

Recently uploaded

Comparative structure of adrenal gland in vertebrates
Comparative structure of adrenal gland in vertebratesComparative structure of adrenal gland in vertebrates
Comparative structure of adrenal gland in vertebrates
sachin783648
 
Body fluids_tonicity_dehydration_hypovolemia_hypervolemia.pptx
Body fluids_tonicity_dehydration_hypovolemia_hypervolemia.pptxBody fluids_tonicity_dehydration_hypovolemia_hypervolemia.pptx
Body fluids_tonicity_dehydration_hypovolemia_hypervolemia.pptx
muralinath2
 
platelets- lifespan -Clot retraction-disorders.pptx
platelets- lifespan -Clot retraction-disorders.pptxplatelets- lifespan -Clot retraction-disorders.pptx
platelets- lifespan -Clot retraction-disorders.pptx
muralinath2
 
EY - Supply Chain Services 2018_template.pptx
EY - Supply Chain Services 2018_template.pptxEY - Supply Chain Services 2018_template.pptx
EY - Supply Chain Services 2018_template.pptx
AlguinaldoKong
 
ESR_factors_affect-clinic significance-Pathysiology.pptx
ESR_factors_affect-clinic significance-Pathysiology.pptxESR_factors_affect-clinic significance-Pathysiology.pptx
ESR_factors_affect-clinic significance-Pathysiology.pptx
muralinath2
 
in vitro propagation of plants lecture note.pptx
in vitro propagation of plants lecture note.pptxin vitro propagation of plants lecture note.pptx
in vitro propagation of plants lecture note.pptx
yusufzako14
 
What is greenhouse gasses and how many gasses are there to affect the Earth.
What is greenhouse gasses and how many gasses are there to affect the Earth.What is greenhouse gasses and how many gasses are there to affect the Earth.
What is greenhouse gasses and how many gasses are there to affect the Earth.
moosaasad1975
 
Leaf Initiation, Growth and Differentiation.pdf
Leaf Initiation, Growth and Differentiation.pdfLeaf Initiation, Growth and Differentiation.pdf
Leaf Initiation, Growth and Differentiation.pdf
RenuJangid3
 
platelets_clotting_biogenesis.clot retractionpptx
platelets_clotting_biogenesis.clot retractionpptxplatelets_clotting_biogenesis.clot retractionpptx
platelets_clotting_biogenesis.clot retractionpptx
muralinath2
 
4. An Overview of Sugarcane White Leaf Disease in Vietnam.pdf
4. An Overview of Sugarcane White Leaf Disease in Vietnam.pdf4. An Overview of Sugarcane White Leaf Disease in Vietnam.pdf
4. An Overview of Sugarcane White Leaf Disease in Vietnam.pdf
ssuserbfdca9
 
filosofia boliviana introducción jsjdjd.pptx
filosofia boliviana introducción jsjdjd.pptxfilosofia boliviana introducción jsjdjd.pptx
filosofia boliviana introducción jsjdjd.pptx
IvanMallco1
 
In silico drugs analogue design: novobiocin analogues.pptx
In silico drugs analogue design: novobiocin analogues.pptxIn silico drugs analogue design: novobiocin analogues.pptx
In silico drugs analogue design: novobiocin analogues.pptx
AlaminAfendy1
 
SCHIZOPHRENIA Disorder/ Brain Disorder.pdf
SCHIZOPHRENIA Disorder/ Brain Disorder.pdfSCHIZOPHRENIA Disorder/ Brain Disorder.pdf
SCHIZOPHRENIA Disorder/ Brain Disorder.pdf
SELF-EXPLANATORY
 
role of pramana in research.pptx in science
role of pramana in research.pptx in sciencerole of pramana in research.pptx in science
role of pramana in research.pptx in science
sonaliswain16
 
Hemostasis_importance& clinical significance.pptx
Hemostasis_importance& clinical significance.pptxHemostasis_importance& clinical significance.pptx
Hemostasis_importance& clinical significance.pptx
muralinath2
 
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...
Ana Luísa Pinho
 
Cancer cell metabolism: special Reference to Lactate Pathway
Cancer cell metabolism: special Reference to Lactate PathwayCancer cell metabolism: special Reference to Lactate Pathway
Cancer cell metabolism: special Reference to Lactate Pathway
AADYARAJPANDEY1
 
Hemoglobin metabolism_pathophysiology.pptx
Hemoglobin metabolism_pathophysiology.pptxHemoglobin metabolism_pathophysiology.pptx
Hemoglobin metabolism_pathophysiology.pptx
muralinath2
 
Astronomy Update- Curiosity’s exploration of Mars _ Local Briefs _ leadertele...
Astronomy Update- Curiosity’s exploration of Mars _ Local Briefs _ leadertele...Astronomy Update- Curiosity’s exploration of Mars _ Local Briefs _ leadertele...
Astronomy Update- Curiosity’s exploration of Mars _ Local Briefs _ leadertele...
NathanBaughman3
 
RNA INTERFERENCE: UNRAVELING GENETIC SILENCING
RNA INTERFERENCE: UNRAVELING GENETIC SILENCINGRNA INTERFERENCE: UNRAVELING GENETIC SILENCING
RNA INTERFERENCE: UNRAVELING GENETIC SILENCING
AADYARAJPANDEY1
 

Recently uploaded (20)

Comparative structure of adrenal gland in vertebrates
Comparative structure of adrenal gland in vertebratesComparative structure of adrenal gland in vertebrates
Comparative structure of adrenal gland in vertebrates
 
Body fluids_tonicity_dehydration_hypovolemia_hypervolemia.pptx
Body fluids_tonicity_dehydration_hypovolemia_hypervolemia.pptxBody fluids_tonicity_dehydration_hypovolemia_hypervolemia.pptx
Body fluids_tonicity_dehydration_hypovolemia_hypervolemia.pptx
 
platelets- lifespan -Clot retraction-disorders.pptx
platelets- lifespan -Clot retraction-disorders.pptxplatelets- lifespan -Clot retraction-disorders.pptx
platelets- lifespan -Clot retraction-disorders.pptx
 
EY - Supply Chain Services 2018_template.pptx
EY - Supply Chain Services 2018_template.pptxEY - Supply Chain Services 2018_template.pptx
EY - Supply Chain Services 2018_template.pptx
 
ESR_factors_affect-clinic significance-Pathysiology.pptx
ESR_factors_affect-clinic significance-Pathysiology.pptxESR_factors_affect-clinic significance-Pathysiology.pptx
ESR_factors_affect-clinic significance-Pathysiology.pptx
 
in vitro propagation of plants lecture note.pptx
in vitro propagation of plants lecture note.pptxin vitro propagation of plants lecture note.pptx
in vitro propagation of plants lecture note.pptx
 
What is greenhouse gasses and how many gasses are there to affect the Earth.
What is greenhouse gasses and how many gasses are there to affect the Earth.What is greenhouse gasses and how many gasses are there to affect the Earth.
What is greenhouse gasses and how many gasses are there to affect the Earth.
 
Leaf Initiation, Growth and Differentiation.pdf
Leaf Initiation, Growth and Differentiation.pdfLeaf Initiation, Growth and Differentiation.pdf
Leaf Initiation, Growth and Differentiation.pdf
 
platelets_clotting_biogenesis.clot retractionpptx
platelets_clotting_biogenesis.clot retractionpptxplatelets_clotting_biogenesis.clot retractionpptx
platelets_clotting_biogenesis.clot retractionpptx
 
4. An Overview of Sugarcane White Leaf Disease in Vietnam.pdf
4. An Overview of Sugarcane White Leaf Disease in Vietnam.pdf4. An Overview of Sugarcane White Leaf Disease in Vietnam.pdf
4. An Overview of Sugarcane White Leaf Disease in Vietnam.pdf
 
filosofia boliviana introducción jsjdjd.pptx
filosofia boliviana introducción jsjdjd.pptxfilosofia boliviana introducción jsjdjd.pptx
filosofia boliviana introducción jsjdjd.pptx
 
In silico drugs analogue design: novobiocin analogues.pptx
In silico drugs analogue design: novobiocin analogues.pptxIn silico drugs analogue design: novobiocin analogues.pptx
In silico drugs analogue design: novobiocin analogues.pptx
 
SCHIZOPHRENIA Disorder/ Brain Disorder.pdf
SCHIZOPHRENIA Disorder/ Brain Disorder.pdfSCHIZOPHRENIA Disorder/ Brain Disorder.pdf
SCHIZOPHRENIA Disorder/ Brain Disorder.pdf
 
role of pramana in research.pptx in science
role of pramana in research.pptx in sciencerole of pramana in research.pptx in science
role of pramana in research.pptx in science
 
Hemostasis_importance& clinical significance.pptx
Hemostasis_importance& clinical significance.pptxHemostasis_importance& clinical significance.pptx
Hemostasis_importance& clinical significance.pptx
 
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...
 
Cancer cell metabolism: special Reference to Lactate Pathway
Cancer cell metabolism: special Reference to Lactate PathwayCancer cell metabolism: special Reference to Lactate Pathway
Cancer cell metabolism: special Reference to Lactate Pathway
 
Hemoglobin metabolism_pathophysiology.pptx
Hemoglobin metabolism_pathophysiology.pptxHemoglobin metabolism_pathophysiology.pptx
Hemoglobin metabolism_pathophysiology.pptx
 
Astronomy Update- Curiosity’s exploration of Mars _ Local Briefs _ leadertele...
Astronomy Update- Curiosity’s exploration of Mars _ Local Briefs _ leadertele...Astronomy Update- Curiosity’s exploration of Mars _ Local Briefs _ leadertele...
Astronomy Update- Curiosity’s exploration of Mars _ Local Briefs _ leadertele...
 
RNA INTERFERENCE: UNRAVELING GENETIC SILENCING
RNA INTERFERENCE: UNRAVELING GENETIC SILENCINGRNA INTERFERENCE: UNRAVELING GENETIC SILENCING
RNA INTERFERENCE: UNRAVELING GENETIC SILENCING
 

Genome sequencing and the development of our current information library

  • 1. Genome projects and the development of our current information library  Name: Zarlish Attique  Roll no: 187104  BS: Bioinformatics  Semester: 5th  Subject: Genomics  Teacher: Muhammad Rizwan  Date: 12,January,2020 Government Post Graduate College Mandian Abbottabad Power point slides created by Zarlish Attique
  • 2. Table of Contents • Genome projects • Different types of genome projects • Genome projects for five kingdom classification • Methods use for genome projects • Current information library and conclusion
  • 3. Genome Projects Scientific endeavors ultimately aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features. 1. Genome Assembly: the process of taking a large number of short DNA sequences and putting them back together to create a representation of the original chromosomes from which the DNA originated. 2. Genome annotation: the process of identifying attaching biological information to sequences , and particularly in identifying the locations of genes and determining what those genes do. Figure: Represents different important stages and involvements in the genome projects. Genome Projects and development of our current information library 3
  • 4. Some genome projects o Genomic Science Program: microbes and plants at the molecular, cellular, and community levels. a predictive understanding of how living systems operate. https://genomicscience.energy.gov/ o ENCODE: ENCyclopedia of DNA Elements: In September 2003, to carry out a project to identify all functional elements in the human genome sequence. o The 100,000 Genomes Project Wellcome Trust Sanger Institute in Hinxton; the Beijing Genomics Institute Shenzhen; and the US NIH National Human Genome Research Institute. https://www.internationalgenome.org/data Genome Projects and development of our current information library 4
  • 5. Some genome projects o Roadmap Epigenomics Project: Producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research and to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts. http://www.roadmapepigenomics.org/ o Genographic Project: Led by National Geographic and IBM: technologies to analyze historical patterns in DNA from participants around the world to better understand our human genetic roots. https://www.nationalgeographic.com/sorry/genographic o Knockout Mouse Phenotyping Program (KOMP2): Leading the way as part of the International Mouse Phenotyping Consortium (IMPC) in understanding the aging process and diseases that occur later in life. Genome Projects and development of our current information library 5
  • 6. Some genome projects o International HapMap Project: a haplotype map of the human genome: to find genes affecting health, disease, and responses to drugs and environmental factors. http://www.hapmap.org/ o Microbial Genome Project: U.S. Department of Energy (DOE) led the Microbial Genome Project from 1994- 2005.:finding alternative sources of energy, understanding biological carbon cycling. o Environmental Genome Project: complex inter- relationship between multiple genetic and environmental factors. Goal of the EGP is to characterize how specific human genetic variations, or polymorphisms, contribute to environmentally induced disease susceptibility. https://www.niehs.nih.gov/ Genome Projects and development of our current information library 6
  • 7. Some genome projects o Cancer Genome Anatomy Project: to determine the gene expression profiles of normal, precancer, and cancer cells, leading eventually to improved detection, diagnosis, and treatment for the patient. https://cgap.nci.nih.gov/ o Chimpanzee genome Project: by comparing the genomes of humans and other apes, to better understand what makes humans distinct from other species from a genetic perspective, published in Nature on September 1, 2005, there are differences between human and chimpanzee genes. o 100K Pathogen Genome Project: launched in July 2012, infectious microorganisms to create a database of bacterial genome sequences for use in public health, outbreak detection, and bacterial pathogen detection. https://www.internationalgenome.org/data Genome Projects and development of our current information library 7
  • 8. Species Strain Base Pairs Genes Akkermansia muciniphila ATCC BAA-835 2,664,102 2,176 Akkermansia muciniphila Urmite 2,664,714 2,192 Chlamydia muridarum Nigg 1,072,950 904 Chlamydia trachomatis AHAR13 1,044,459 911 Chlamydia trachomatis DUW 1,042,519 894 Chlamydophila abortus S26-3 1,144,377 961 MONERA Following are the sequenced genomes of monerans. Genome Projects and development of our current information library 8
  • 9. Protists Following are the six earliest sequenced genomes of protists. Organism Genome size Organization Year of completion Guillardia theta 0.551 Mb Canadian Institute of Advanced Research, Philipps-University Marburg and the University of British Columbia 2001 Plasmodium falciparum Clone:3D7 22.9 Mb Malaria Genome Project Consortium 2002 Plasmodium yoelii yoelii Strain:17XNL 23.1 Mb TIGR and NMRC 2002 Cryptosporidium hominis Strain:TU502 10.4 Mb Virginia Commonwealth University 2004 Cryptosporidium parvum C- or genotype 2 isolate 16.5 Mb UCSF and University of Minnesota 2004 Thalassiosira pseudonana Strain:CCMP 1335 34.5 Mb Joint Genome Institute and the University of Washington 2004 Genome Projects and development of our current information library 9
  • 10. Plants Following are the five earliest sequenced genomes of plants. Organism Genome size Organization Year of completion Arabidopsis thaliana Ecotype:Columbia 135 Mb Arabidopsis Genome Initiative 2000 Cyanidioschyzon merolae Strain:10D 16.5 Mb University of Tokyo, Rikkyo University, Saitama University and Kumamoto University 2004 Oryza sativa ssp indica 420 Mb Beijing Genomics Institute, Zhejiang University and the Chinese Academy of Sciences 2002 Ostreococcus tauri 12.6 Mb Laboratoire Arago 2006 Populus trichocarpa 550 Mb The International Poplar Genome Consortium 2006 Genome Projects and development of our current information library 10
  • 11. Fungi Organism Genome size Organization Year of completion Saccharomyces cerevisiae Strain:S288C 12.1 Mb International Collaboration for the Yeast Genome Sequencing 1996 Encephalitozoon cuniculi 2.9 Mb Genoscope and Université Blaise Pascal 2001 Schizosaccharomyces pombe Strain:972h- 14 Mb Sanger Institute and Cold Spring Harbor Laboratory 2002 Neurospora crassa 40 Mb Broad Institute Oregon Health and science university, University of Kentucky, and the University of Kansas 2003 Phanerochaete chrysosporium Strain:RP78 Imagine! 30 Mb Joint Genome Institute 2004 Following are the five earliest sequenced genomes of fungi. Genome Projects and development of our current information library 11
  • 12. Animals Following are the five earliest sequenced genomes of animals. Organism Genome size Number of genes predicted Organization Year of completion Caenorhabditis elegans Strain:Bristol N2 100 Mb 19,000 Washington University and the Sanger Institute 199 Drosophila melanogaster 165 Mb 13,600 Celera, UC Berkeley, Baylor College of Medicine, European DGP 2000 Anopheles gambiae Strain: PEST 278 Mb 13,683 Celera Genomics and Genoscope 2002 Takifugu rubripes 390 Mb 22–29,000 International Fugu Genome Consortium 2002 Homo sapiens 3.2 Gb 18,826 (CCDS consortium) Human Genome Project Consortium and Celera Genomics Draft 2001 Complete 2006 Genome Projects and development of our current information library 12
  • 13. Viruses Organism Genome size (base pairs) Note Porcine circovirus type 1 1,759 1.8kb Smallest viruses replicating autonomously in eukaryotic cells. Bacteriophage MS2 3,569 3.5kb First sequenced RNA-genome SV40 5,224 5.2kb Phage Φ-X174 5,386 5.4kb First sequenced DNA-genome HIV 9,749 9.7kb Phage λ 48,502 48.5kb Often used as a vector for the cloning of recombinant DNA. Following are the sequenced genomes of viruses. Genome Projects and development of our current information library 13
  • 14. High-throughput sequencing Genome Projects and development of our current information library 14
  • 15. High-throughput sequencing Genome Projects and development of our current information library 15
  • 16. High-throughput sequencing Genome Projects and development of our current information library 16
  • 17. High-throughput sequencing Genome Projects and development of our current information library 17
  • 18. High-throughput sequencing Genome Projects and development of our current information library 18
  • 19. De novo sequencing Genome Projects and development of our current information library 19
  • 20. Resequencing Genome Projects and development of our current information library 20
  • 22. Genome Annotation • http://www.repeatmasker.org/ • Types of repeats found in the genome, Regulatory elements, Homologues in other species,ORF etc. Genome Projects and development of our current information library 22 Name Can be Used For GeneMark Archaea, Metagenomes ,Eukaryotes,Viruses, Phages, Plasmids, EST and cDNA GeneHacker Microbial genomes GeneWalker Human HMMgene (v. 1.1) vertebrate and C. elegans Chemgenome2.0 Prokaryotes Softberry Server Bacteria ,Viruses and eukaryotes Gene ID Animal, Human, Plants fungus, Protists GenScan Vertebrates, Arabidopsis, Maize
  • 24. Current information library 1. The past few years have seen truly astounding progress in the development of high-throughput sequencing techniques. 2. Initial determination of a draft of the human genome took ten years, at an estimated cost of $US 3 ´ 109. 3. Now instruments exist that can produce 250 Gb per week. 4. Currently in Shenzhen – has 128 such instruments. Each can produce 25 ´ 109 bp per day! This corresponds to one human genome at over 8X coverage. Running at full capacity, these resources could produce 10 000 human genomes per year. 5. Moreover, there is no reason to think that the technical progress will not continue to accelerate. 6. Two aspects of a large-scale sequencing project. 7. One is the generation of the raw data. Most methods sequence long DNA molecules by fragmenting them, and partially sequencing the pieces. 8. Both generation of raw data, and assembly, depend crucially on effective and efficient computer programs.
  • 25. References 1. https://www.sciencedirect.com/topics/neuroscience/genome-project 2. https://www.nature.com/articles/nbt1000_1049 3. https://benthamscience.com/journals/current-bioinformatics/library-recommendations/ 4. https://www.studocu.com/en-us/document/california-institute-of-technology/human- genetics-and-genomics/other/introduction-to-genomics-second-edition-arthur-m- lesk/1587322/view 5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1525323/ Any Question: Feel free to ask! Genome Projects and development of our current information library 25