12-04-2011, 09:24 AM
Presented by:
Mr. D. M. Patil
[attachment=12050]
Definitions
• Bioinformatics is an integration of computer knowledge, mathematical and statistical methods to manage and analyze the biological information.
• Bioinformatics is currently defined as the study of information content and information flow in biological systems and processes.
• The science of developing computer databases and algorithms for the purpose of speeding up and enhancing biological research.
• Bioinformatics focuses more on the development of practical tools for biological data management and analysis
Bioinformatics evolved to deal with four related but still distinct works namely:
1. Handling and management of biological data including its organization, control, analysis and so forth.
2. Communication among people, projects and institutions engaged in biological research and applications. This may include email, file transfer, remote login, computer conferencing and establishment of web based information resources.
3. Organization, access, search and retrieval of biological information, documents and literature.
4. Analysis and interpretation of the biological data through the computational approaches including visualization, mathematical modeling and development of algorithms for highly processing of complex biological structures.
Application areas of bioinformatics:
• Post-genome applications
• Sequence analysis
• Protein structure prediction
• Data processing, data management
• Database searches
• Phylogenetic analysis
• Gene expression
• Recognition of genes and regulatory elements
• Modeling and simulation of metabolic pathways and regulatory networks
• Software tools
Human Genome Project
• Just a half-century ago very little was known about the genetic factors that contribute to human disease.
• In 1953, James Watson and Francis Crick described the double helix structure of deoxyribonucleic acid (DNA), the chemical compound that contains the genetic instructions for building, running and maintaining living organisms.
• Until the early 1970’s, DNA was the most difficult cellular molecule for biochemists to analyze.
• DNA is now the easiest molecule to analyze – we can now isolate a specific region of the genome, produce a virtually unlimited number of copies of it, and determine its nucleotide sequence overnight.
The human genome is made up of approximately three billion base pairs of deoxyribonucleic acid (DNA). The bases of DNA are adenine (A), thymine (T), guanine (G), and cytosine ©.
• In 1990, the National Institutes of Health (NIH) and the US. Department of Energy joined with international partners in a quest to sequence all 3 billion letters, or base pairs, in the human genome, which is the complete set of DNA in the human body. This concerted, public effort was the Human Genome Project.
Who is the U.S. Human Genome Project?
National Center for Human Genome Research
• Department of Energy (DOE) - Ari Patrinos
• National Institutes of Health(NIH)- Francis Collins
Where
• DOE Joint Genome Institute
3 DOE national labs
• Baylor College of Medicine
• Sanger Centre
• Washington University Genome Sequencing Center
• Whitehead Institute/MIT Center for Genome Research
Where locally?
• University of Washington Genome Center
• University of Washington Multimegabase Sequencing Center
Whose?
• A reference sequence - not an exact match for any one person
• Blood (female) or sperm (male) samples taken from a large number of donors.
• Ethnically diverse
• Few samples processed
• Names protected
Goals:
• identify all the approximate 30,000 genes in human DNA,
• determine the sequences of the 3 billion chemical base pairs that make up human DNA,
• store this information in databases,
• improve tools for data analysis,
• transfer related technologies to the private sector, and
• address the ethical, legal, and social issues (ELSI) that may arise from the project.
An Independent Genome Project? 1998
• Celera Genomics Corporation CEO- Craig Venter
• Proposes to sequence human genome in 3 years for $3 million
• Invented new sequencing technologies
Milestones:
■ 1990: Project initiated as joint effort of U.S. Department of Energy and the National Institutes of Health
■ June 2000: Completion of a working draft of the entire human genome (covers >90% of the genome)
■ February 2001: Analyses of the working draft are published (First draft published in Science and Nature in February, 2001)
■ April 2003: HGP sequencing is completed and Project is declared finished two years ahead of schedule
Finished Human Genome sequence published in Nature 2003.
• The Human Genome Project’s goal was to provide researchers with powerful tools to understand the genetic factors in human disease, paving the way for new strategies for their diagnosis, treatment and prevention.
• From the start, the Human Genome Project supported an Ethical, Legal and Social Implications research program to address the many complex issues that might arise from this science.
• All data generated by the Human Genome Project were made freely and rapidly available on the Internet, serving to accelerate the pace of medical discovery around the globe.
• In April 2003, researchers successfully completed the Human Genome Project, under budget and more than two years ahead of schedule.
• Sequencing Progress Draft Sequence:
Completed June 26, 2000
• Joint announcement by Venter and Collins
What does the draft human genome sequence tell us?
By the Numbers
• The human genome contains 3 billion chemical nucleotide bases (A, C, T, and G).
• The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases.
• The total number of genes is estimated at around 30,000 to 40,000.
• Almost all (99.9%) nucleotide bases are exactly the same in all people.
• The functions are unknown for over 50% of discovered genes.
• Total length 3000 Mb
• ~ 40,000 genes (coding seq)
• Gene sequences < 5%
– Exons ~ 1.5% (coding)
– Introns ~ 3.5% (noncoding)
– Intergenic regions (junk) > 95%
– Repeats > 50%
How It's Arranged
• The human genome's gene-dense "urban centers" are predominantly composed of the DNA building blocks G and C.
• In contrast, the gene-poor "deserts" are rich in the DNA building blocks A and T. GC- and AT-rich regions usually can be seen through a microscope as light and dark bands on chromosomes.
• Genes appear to be concentrated in random areas along the genome, with vast expanses of non coding DNA between.
• Stretches of up to 30,000 C and G bases repeating over and over often occur adjacent to gene-rich areas, forming a barrier between the genes and the "junk DNA.”
• Chromosome 1 has the most genes (2968), and the Y chromosome has the fewest (231).
The Wheat from the Chaff
• Less than 2% of the genome codes for proteins.
• Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome.
• Repetitive sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics. Over time, these repeats reshape the genome by rearranging it, creating entirely new genes, and modifying and reshuffling existing genes.
• These genomes were sequenced by 2003
Genome Sizes (MegaBases)
• Model organisms
• Bacteria (E. coli, influenza, several others)
• Yeast (Saccharomyces cerevisiae)
• Plant (Arabidopsis thaliana)
• Roundworm (Caenorhabditis elegans)
• Fruit fly (Drosophila melanogaster)
• Mouse (Mus musculus)
Mr. D. M. Patil
[attachment=12050]
Definitions
• Bioinformatics is an integration of computer knowledge, mathematical and statistical methods to manage and analyze the biological information.
• Bioinformatics is currently defined as the study of information content and information flow in biological systems and processes.
• The science of developing computer databases and algorithms for the purpose of speeding up and enhancing biological research.
• Bioinformatics focuses more on the development of practical tools for biological data management and analysis
Bioinformatics evolved to deal with four related but still distinct works namely:
1. Handling and management of biological data including its organization, control, analysis and so forth.
2. Communication among people, projects and institutions engaged in biological research and applications. This may include email, file transfer, remote login, computer conferencing and establishment of web based information resources.
3. Organization, access, search and retrieval of biological information, documents and literature.
4. Analysis and interpretation of the biological data through the computational approaches including visualization, mathematical modeling and development of algorithms for highly processing of complex biological structures.
Application areas of bioinformatics:
• Post-genome applications
• Sequence analysis
• Protein structure prediction
• Data processing, data management
• Database searches
• Phylogenetic analysis
• Gene expression
• Recognition of genes and regulatory elements
• Modeling and simulation of metabolic pathways and regulatory networks
• Software tools
Human Genome Project
• Just a half-century ago very little was known about the genetic factors that contribute to human disease.
• In 1953, James Watson and Francis Crick described the double helix structure of deoxyribonucleic acid (DNA), the chemical compound that contains the genetic instructions for building, running and maintaining living organisms.
• Until the early 1970’s, DNA was the most difficult cellular molecule for biochemists to analyze.
• DNA is now the easiest molecule to analyze – we can now isolate a specific region of the genome, produce a virtually unlimited number of copies of it, and determine its nucleotide sequence overnight.
The human genome is made up of approximately three billion base pairs of deoxyribonucleic acid (DNA). The bases of DNA are adenine (A), thymine (T), guanine (G), and cytosine ©.
• In 1990, the National Institutes of Health (NIH) and the US. Department of Energy joined with international partners in a quest to sequence all 3 billion letters, or base pairs, in the human genome, which is the complete set of DNA in the human body. This concerted, public effort was the Human Genome Project.
Who is the U.S. Human Genome Project?
National Center for Human Genome Research
• Department of Energy (DOE) - Ari Patrinos
• National Institutes of Health(NIH)- Francis Collins
Where
• DOE Joint Genome Institute
3 DOE national labs
• Baylor College of Medicine
• Sanger Centre
• Washington University Genome Sequencing Center
• Whitehead Institute/MIT Center for Genome Research
Where locally?
• University of Washington Genome Center
• University of Washington Multimegabase Sequencing Center
Whose?
• A reference sequence - not an exact match for any one person
• Blood (female) or sperm (male) samples taken from a large number of donors.
• Ethnically diverse
• Few samples processed
• Names protected
Goals:
• identify all the approximate 30,000 genes in human DNA,
• determine the sequences of the 3 billion chemical base pairs that make up human DNA,
• store this information in databases,
• improve tools for data analysis,
• transfer related technologies to the private sector, and
• address the ethical, legal, and social issues (ELSI) that may arise from the project.
An Independent Genome Project? 1998
• Celera Genomics Corporation CEO- Craig Venter
• Proposes to sequence human genome in 3 years for $3 million
• Invented new sequencing technologies
Milestones:
■ 1990: Project initiated as joint effort of U.S. Department of Energy and the National Institutes of Health
■ June 2000: Completion of a working draft of the entire human genome (covers >90% of the genome)
■ February 2001: Analyses of the working draft are published (First draft published in Science and Nature in February, 2001)
■ April 2003: HGP sequencing is completed and Project is declared finished two years ahead of schedule
Finished Human Genome sequence published in Nature 2003.
• The Human Genome Project’s goal was to provide researchers with powerful tools to understand the genetic factors in human disease, paving the way for new strategies for their diagnosis, treatment and prevention.
• From the start, the Human Genome Project supported an Ethical, Legal and Social Implications research program to address the many complex issues that might arise from this science.
• All data generated by the Human Genome Project were made freely and rapidly available on the Internet, serving to accelerate the pace of medical discovery around the globe.
• In April 2003, researchers successfully completed the Human Genome Project, under budget and more than two years ahead of schedule.
• Sequencing Progress Draft Sequence:
Completed June 26, 2000
• Joint announcement by Venter and Collins
What does the draft human genome sequence tell us?
By the Numbers
• The human genome contains 3 billion chemical nucleotide bases (A, C, T, and G).
• The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases.
• The total number of genes is estimated at around 30,000 to 40,000.
• Almost all (99.9%) nucleotide bases are exactly the same in all people.
• The functions are unknown for over 50% of discovered genes.
• Total length 3000 Mb
• ~ 40,000 genes (coding seq)
• Gene sequences < 5%
– Exons ~ 1.5% (coding)
– Introns ~ 3.5% (noncoding)
– Intergenic regions (junk) > 95%
– Repeats > 50%
How It's Arranged
• The human genome's gene-dense "urban centers" are predominantly composed of the DNA building blocks G and C.
• In contrast, the gene-poor "deserts" are rich in the DNA building blocks A and T. GC- and AT-rich regions usually can be seen through a microscope as light and dark bands on chromosomes.
• Genes appear to be concentrated in random areas along the genome, with vast expanses of non coding DNA between.
• Stretches of up to 30,000 C and G bases repeating over and over often occur adjacent to gene-rich areas, forming a barrier between the genes and the "junk DNA.”
• Chromosome 1 has the most genes (2968), and the Y chromosome has the fewest (231).
The Wheat from the Chaff
• Less than 2% of the genome codes for proteins.
• Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome.
• Repetitive sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics. Over time, these repeats reshape the genome by rearranging it, creating entirely new genes, and modifying and reshuffling existing genes.
• These genomes were sequenced by 2003
Genome Sizes (MegaBases)
• Model organisms
• Bacteria (E. coli, influenza, several others)
• Yeast (Saccharomyces cerevisiae)
• Plant (Arabidopsis thaliana)
• Roundworm (Caenorhabditis elegans)
• Fruit fly (Drosophila melanogaster)
• Mouse (Mus musculus)
