Metagenomics analysis
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Metagenomics is the study of microbial communities directly from environmental samples without culturing individual species. It sequences all DNA from a sample simultaneously, bypassing the need for culture. Analysis of metagenomic data involves screening and phylogenetic studies of the large amounts of sequence data. Metagenomics can provide insights into microbial community structure and interactions, and discover novel enzymes and genes with industrial or pharmaceutical applications. Challenges include DNA purification issues, contamination, sequencing errors, and difficulties assembling less abundant genomes from immense metagenomic datasets.
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Metagenomics
This document discusses the field of metagenomics, which involves directly extracting and sequencing genetic material from environmental samples without culturing individual microbial species. It provides a brief history of metagenomics from early microbiologists in the 17th century to recent large-scale sequencing projects. Methods of metagenomic analysis like sequence-driven and function-driven approaches are described. Applications to studying uncultured symbiotic microbes, extreme environments, and the human gut microbiome are also summarized.
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental samples. Metagenomics is a molecular tool used to analyse DNA acquired from environmental samples, in order to study the community of microorganisms present, without the necessity of obtaining pure cultures.
Metagenomics
Microbiology has experienced a transformation during the last 25 years that has altered microbiologists' view of microorganisms and how to study them. The realization that most microorganisms cannot be grown readily in pure culture forced microbiologists to question their belief that the microbial world had been conquered. We were forced to replace this belief with an acknowledgment of the extent of our ignorance about the range of metabolic and organismal diversity.
Genomics
This document provides an overview of genomics, including its history, major research areas, and applications. Genomics is concerned with studying the genomes of organisms, including determining entire DNA sequences and genetic mapping. Major research areas discussed include bacteriophage, human, computational, and comparative genomics. Applications of genomics discussed include functional genomics, predictive medicine, metagenomics for medicine, biofuels and more. The first genomes sequenced were small viruses and mitochondria, while the human genome project aimed to map the entire human DNA sequence.
Metagenomics and it’s applications
Shotgun metagenomics sequencing allows researchers to comprehensively sample all genes in organisms present in a complex sample without culturing. This provides insights into bacterial diversity, abundance, and uncultured microbes. Bioinformatics pipelines guide analysis including quality filtering, assembly, binning, gene finding, fingerprinting, and phylogeny/diversity modeling to understand communities. Metagenomics has applications in antibiotic/drug discovery, bioremediation, agriculture, human microbiome mapping, and more. Tools like QIIME, Mothur, MEGAN, and MG-RAST facilitate large-scale metagenomic analysis.
Metagenomic analysis
This document provides an overview of metagenomic analysis. It discusses collecting metagenomic data through sampling and sequencing environmental samples. It then covers various bioinformatics approaches used in metagenomic analysis such as assembly, binning, and annotation of sequencing data. Specific tools and algorithms for these approaches are also described, including reference-based and de novo assembly, compositional and similarity-based binning methods like AbundanceBin.
Structural genomics
Structural genomics aims to determine the 3D structure of all proteins in a genome. It uses high-throughput methods like X-ray crystallography and NMR on a genomic scale. This allows determination of protein structures for entire proteomes. It provides insights into protein function and can aid drug discovery by identifying potential drug targets like in Mycobacterium tuberculosis. Structural genomics leverages completed genome sequences to clone and express all encoded proteins for structural characterization.
High-Throughput Sequencing
Talk on High-Throughput Sequencing: Overview and Selected Applications for Masters students. Nov 9th 2011
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Metagenomics
This document discusses the field of metagenomics, which involves directly extracting and sequencing genetic material from environmental samples without culturing individual microbial species. It provides a brief history of metagenomics from early microbiologists in the 17th century to recent large-scale sequencing projects. Methods of metagenomic analysis like sequence-driven and function-driven approaches are described. Applications to studying uncultured symbiotic microbes, extreme environments, and the human gut microbiome are also summarized.
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental samples. Metagenomics is a molecular tool used to analyse DNA acquired from environmental samples, in order to study the community of microorganisms present, without the necessity of obtaining pure cultures.
Metagenomics
Microbiology has experienced a transformation during the last 25 years that has altered microbiologists' view of microorganisms and how to study them. The realization that most microorganisms cannot be grown readily in pure culture forced microbiologists to question their belief that the microbial world had been conquered. We were forced to replace this belief with an acknowledgment of the extent of our ignorance about the range of metabolic and organismal diversity.
Genomics
This document provides an overview of genomics, including its history, major research areas, and applications. Genomics is concerned with studying the genomes of organisms, including determining entire DNA sequences and genetic mapping. Major research areas discussed include bacteriophage, human, computational, and comparative genomics. Applications of genomics discussed include functional genomics, predictive medicine, metagenomics for medicine, biofuels and more. The first genomes sequenced were small viruses and mitochondria, while the human genome project aimed to map the entire human DNA sequence.
Metagenomics and it’s applications
Shotgun metagenomics sequencing allows researchers to comprehensively sample all genes in organisms present in a complex sample without culturing. This provides insights into bacterial diversity, abundance, and uncultured microbes. Bioinformatics pipelines guide analysis including quality filtering, assembly, binning, gene finding, fingerprinting, and phylogeny/diversity modeling to understand communities. Metagenomics has applications in antibiotic/drug discovery, bioremediation, agriculture, human microbiome mapping, and more. Tools like QIIME, Mothur, MEGAN, and MG-RAST facilitate large-scale metagenomic analysis.
Metagenomic analysis
This document provides an overview of metagenomic analysis. It discusses collecting metagenomic data through sampling and sequencing environmental samples. It then covers various bioinformatics approaches used in metagenomic analysis such as assembly, binning, and annotation of sequencing data. Specific tools and algorithms for these approaches are also described, including reference-based and de novo assembly, compositional and similarity-based binning methods like AbundanceBin.
Structural genomics
Structural genomics aims to determine the 3D structure of all proteins in a genome. It uses high-throughput methods like X-ray crystallography and NMR on a genomic scale. This allows determination of protein structures for entire proteomes. It provides insights into protein function and can aid drug discovery by identifying potential drug targets like in Mycobacterium tuberculosis. Structural genomics leverages completed genome sequences to clone and express all encoded proteins for structural characterization.
High-Throughput Sequencing
Talk on High-Throughput Sequencing: Overview and Selected Applications for Masters students. Nov 9th 2011
Metagenomics by microbiology dept. panjab university2018copy
Metagenomics is the genomic analysis of microorganisms in an environmental sample without culturing. It allows researchers to study unculturable microbes by extracting DNA directly from samples and sequencing it. While metagenomics has advanced our understanding of microbial diversity, challenges remain in expressing genes from uncultured organisms in a surrogate host for functional screening.
Comparative genomics
Comparative genomics involves systematically comparing genome sequences from different organisms. It uses computer programs to identify homologous genomic regions and align sequences at the base-pair level. Comparing genomes at different phylogenetic distances can provide insights into gene structure/function, evolution, and characteristics unique to each organism. Key tools for comparative genomics include genome browsers, aligners, and databases that classify orthologous gene clusters conserved across species.
Functional genomics
This document provides an overview of functional genomics and methods for transcriptome analysis. It discusses two main approaches - sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. For sequence-based approaches, it describes how ESTs can provide gene discovery and expression information but have limitations. It outlines the SAGE methodology and gene index construction to organize EST data. For microarrays, it summarizes the basic workflow including sample preparation, hybridization, image analysis and data normalization to identify differentially expressed genes through statistical tests.
2 whole genome sequencing and analysis
Whole genome sequencing is the process of determining the complete DNA sequence of an organism's genome. It involves sequencing all chromosomal and organellar DNA. Key methods include shotgun sequencing, which randomly fragments DNA for sequencing, and single molecule real time sequencing, which observes individual DNA polymerases incorporating nucleotides in real time using fluorescent tags. Whole genome sequencing has provided insights into evolutionary biology and may help predict disease susceptibility, though technical challenges remain such as fully sequencing repetitive regions.
Genetic mapping
There are several types of mapping used to determine the location and distance between genetic elements and markers on a genome. Genetic mapping uses recombination events to estimate distances between markers. Physical mapping relies on experimental outcomes like hybridization and amplification but may not provide distance measures. Radiation hybrid mapping allows high-resolution mapping by exploiting how rodent cells incorporate genetic material from fused cells. Comparative mapping utilizes animal models and ortholog identification to explore causes of disease across multiple species.
Comparative genomics
Comparative genomics involves comparing genomes to discover similarities and differences. It can provide insights into evolutionary relationships, help predict gene function, and aid in drug discovery. The first step is often aligning genome sequences using tools like BLAST or MUMmer. Genomes can then be compared at various levels, such as overall nucleotide statistics, genome structure, and coding/non-coding regions. Comparing gene and protein content across genomes helps predict functions. Conserved genomic features across species also aid prediction. Insights into genome evolution come from studying molecular events like inversions and duplications. Comparative genomics has impacted phylogenetics and drug target identification.
Comparative genomics
This document provides a summary of a seminar on comparative genomics techniques. It discusses three levels of genome research: structural genomics, functional genomics, and comparative genomics. Comparative genomics involves analyzing and comparing different genomes to study gene content, function, organization, and evolution. Techniques discussed include genome sequencing, mapping, and bioinformatics tools. The document also outlines what can be compared between genomes and how comparative genomics has provided insights into evolution and gene function.
Metagenomic
Metagenomics is the study of genomes recovered from environmental samples without culturing. It involves extracting DNA from an environmental sample and sequencing the DNA. This allows study of the 99% of microbes that cannot be cultured. Metagenomics has applications in discovering new antibiotics, enzymes, and understanding microbial communities and host interactions. It provides a culture-independent way to access genetic diversity and biotechnological potential from uncultured microorganisms.
Yeast Genome
The document summarizes the sequencing of the yeast Saccharomyces cerevisiae genome. Key points:
1) The yeast genome was sequenced between 1989-1996 by over 35 European laboratories in a collaborative effort. By 1996, the entire 12 megabase genome across 16 chromosomes had been sequenced.
2) The genome contains approximately 6,000 open reading frames that were annotated after sequencing. About 30% of yeast genes have homologs in human genes.
3) Sequencing involved creating ordered cosmid libraries, shotgun sequencing, and assembling overlapping sequences into contigs. Genes were identified and analyzed after full genome assembly.
Sequence Submission Tools
In this presentation, I talk about the various tools for the submission of DNA or RNA sequences into various sequence databases. The sequence submission tools talked about in this presentation are BankIt, Sequin and Webin.
Fasta
FASTA is a bioinformatics tool and biological database that is used to compare amino acid sequences of proteins or nucleotide sequences of DNA. It was first described in 1985 by Lipman and Pearson. FASTA performs fast homology searches to find similarities between a query sequence and sequences in a database. While similar to BLAST, FASTA is faster for sequence comparisons. It works by identifying patches of sequence similarity that may contain gaps. Some key FASTA programs include FASTA, TFASTA, FASTS, and FASTX/Y. FASTA is useful for applications like identification of species, establishing phylogeny, DNA mapping, and understanding protein function.
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The European Bioinformatics Institute (EBI) is a center for bioinformatics research and services located in Hinxton, UK. EBI grew out of EMBL's work providing public biological databases and offers major databases on DNA, RNA, proteins, pathways, and more. EBI's website provides access to these databases as well as a variety of bioinformatics tools for sequence analysis, proteomics, microarrays, and more through different channels on their site.
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Genomics is the study of genomes and includes determining entire DNA sequences, genetic mapping, and studying intragenomic phenomena. It allows determining an ideal genotype. Genomics and bioinformatics provide benefits like improved crop productivity, stress tolerance, and nutritional quality. Proteomics studies proteins in cells. Bioinformatics handles large genomic and proteomic data using algorithms. Structural genomics constructs sequence data and maps genes. Functional genomics studies gene function. Comparative genomics compares sequences to find relationships.
Brief history and development of metagenomics
The document provides a brief history of metagenomics, beginning in the 17th century when Antonie van Leeuwenhoek first observed microbes using microscopes. Key developments included the definition of microbial communities, techniques for culturing microorganisms, and the realization that culture-based techniques did not capture total microbial diversity. The field of metagenomics emerged in the late 20th century with developments like PCR, sequencing of 16S rRNA, and shotgun sequencing of environmental samples without culturing. This led to insights into uncultured microbes and their roles in environments like acid mine drainage. Global metagenomic sampling projects helped discover thousands of new microbial species.
Next generation sequencing
This document summarizes a class seminar presentation on next generation sequencing technologies. It begins with an overview of DNA sequencing and its importance. It then reviews the history of sequencing technologies, from the discovery of DNA to the development of Sanger sequencing and next generation sequencing platforms. The document focuses on describing the Illumina/Solexa, 454, and SOLiD next generation sequencing methods. It explains the key steps in library preparation, cluster amplification, and sequencing by synthesis or ligation for these platforms. The advantages of next generation sequencing technologies over Sanger sequencing are also highlighted.
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental samples without culturing organisms. It allows researchers to study the 99.9% of microorganisms that cannot be cultured. Metagenomic analyses of ocean samples revealed over a million new genes and unexpected light-energy pathways in bacteria. Metagenomics has two main approaches - sequence-driven which sequences DNA and compares to databases, and function-driven which screens DNA clones for a desired function. Both approaches have limitations but are complementary. Metagenomics has applications in discovering new antibiotics and enzymes and studying human microbiomes and antibiotic resistance.
Functional genomics
This document discusses functional genomics and its approaches. It defines functional genomics as the worldwide experimental approach to access the function of genes by using information from structural genomics. The key functional genomics approaches discussed are transcriptomics, proteomics, metabolomics, interactomics, epigenetics, and nutrigenomics. Modern techniques discussed include expressed sequence tags (ESTs), serial analysis of gene expression (SAGE), and microarray analysis.
Est database
ESTs are short sequences of DNA that represent genes expressed in certain tissues or organisms. They provide a quick and inexpensive way for scientists to discover new genes and map their positions in genomes. ESTs represent a snapshot of genes expressed in a tissue at a given time. Sequencing the beginning or end of cDNA clones produces 5' and 3' ESTs, which can help identify genes and study gene expression and regulation.
STRUCTURAL GENOMICS, FUNCTIONAL GENOMICS, COMPARATIVE GENOMICS
Structural genomics is a field that aims to determine the 3D structures of all proteins encoded by a genome. It involves determining structures on a large scale using techniques like X-ray crystallography and NMR. This allows identification of novel protein folds and potential drug targets. Comparative genomics compares genomic features between organisms and provides insights into evolution and conserved sequences and functions. It is a key tool in fields like medicine and agriculture.
Bioinformatics and its Applications in Agriculture/Sericulture and in other F...
The National Center for Biotechnology Information (NCBI, 2001) defines bioinformatics as the field of science in which biology, computer science, and information technology merge into a single discipline. Fredj Tekaia defines Bioinformatics the mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information. Bioinformatics has emerged as an essential field of science that is facilitating biological discoveries since more than a decade. Without the usage of bioinformatics tools it is merely impossible to capture, manage process, analyse and interpret the huge amounts data that is available especially after whole genome sequencing projects. The sequencing of the genomes of plants and animals will have enormous benefits for the agricultural community. Bioinformatics tools can be used to search for the genes within these genomes and to elucidate their functions. This specific genetic knowledge could then be used to produce stronger, drought, disease and insect resistant crops and improve the quality. In agriculture it helps in the insect resistance, improve nutritional quality, rational plant improvement, waste cleanup, climate change studies, and development of drought resistance varieties (Dahiya and Lata, 2017) and in addition to this it also plays an important roles in biotechnology, antibiotic resistance, and forensic analysis of microbes, comparative studies, evolutionary studies and veterinary Sciences.
Seri bioinformatics tools and techniques not only facilitated detection of proteomic and genomic diversity among the species/strains, but also resulted in finding a gap in the silkworm genome sequence of a strain that diverged during the course of domestication. Seri-bioinformatics databases are a valuable seri-bioresource. The available online resources on silkworm and its related organisms, including databases as well as informative websites help to make silkworms healthier, more disease resistant and more productive. These databases provides information on gene, protein sequences and diseases and play crucial roles in conservation of the silkworm species and mulberry plants (Singh et al., 216). Bioinformatics approaches give an insight, uncovering the lineage with gene and protein count of B. mori and Drosophila encompass ~18,000 and ~16,000 (Genes) and ~9,000 and ~22,000 (Proteins) respectively (Somshekar and Borgowda, 2013).
Metagenomics
This document discusses metagenomics, which is the study of microbial communities directly in their natural environments without isolating individual species. It outlines some key aspects of metagenomics including that most prokaryotes cannot be cultured, the use of metagenomics to study viral communities, and approaches such as functional screening and sequence-based screening. Limitations and future directions are also mentioned. Metagenomics provides insights into microbial interactions, metabolism, and genomics that were previously unknown.
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Metagenomics is the genomic analysis of microorganisms in an environmental sample without culturing. It allows researchers to study unculturable microbes by extracting DNA directly from samples and sequencing it. While metagenomics has advanced our understanding of microbial diversity, challenges remain in expressing genes from uncultured organisms in a surrogate host for functional screening.
Comparative genomics
Comparative genomics involves systematically comparing genome sequences from different organisms. It uses computer programs to identify homologous genomic regions and align sequences at the base-pair level. Comparing genomes at different phylogenetic distances can provide insights into gene structure/function, evolution, and characteristics unique to each organism. Key tools for comparative genomics include genome browsers, aligners, and databases that classify orthologous gene clusters conserved across species.
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This document provides an overview of functional genomics and methods for transcriptome analysis. It discusses two main approaches - sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. For sequence-based approaches, it describes how ESTs can provide gene discovery and expression information but have limitations. It outlines the SAGE methodology and gene index construction to organize EST data. For microarrays, it summarizes the basic workflow including sample preparation, hybridization, image analysis and data normalization to identify differentially expressed genes through statistical tests.
2 whole genome sequencing and analysis
Whole genome sequencing is the process of determining the complete DNA sequence of an organism's genome. It involves sequencing all chromosomal and organellar DNA. Key methods include shotgun sequencing, which randomly fragments DNA for sequencing, and single molecule real time sequencing, which observes individual DNA polymerases incorporating nucleotides in real time using fluorescent tags. Whole genome sequencing has provided insights into evolutionary biology and may help predict disease susceptibility, though technical challenges remain such as fully sequencing repetitive regions.
Genetic mapping
There are several types of mapping used to determine the location and distance between genetic elements and markers on a genome. Genetic mapping uses recombination events to estimate distances between markers. Physical mapping relies on experimental outcomes like hybridization and amplification but may not provide distance measures. Radiation hybrid mapping allows high-resolution mapping by exploiting how rodent cells incorporate genetic material from fused cells. Comparative mapping utilizes animal models and ortholog identification to explore causes of disease across multiple species.
Comparative genomics
Comparative genomics involves comparing genomes to discover similarities and differences. It can provide insights into evolutionary relationships, help predict gene function, and aid in drug discovery. The first step is often aligning genome sequences using tools like BLAST or MUMmer. Genomes can then be compared at various levels, such as overall nucleotide statistics, genome structure, and coding/non-coding regions. Comparing gene and protein content across genomes helps predict functions. Conserved genomic features across species also aid prediction. Insights into genome evolution come from studying molecular events like inversions and duplications. Comparative genomics has impacted phylogenetics and drug target identification.
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This document provides a summary of a seminar on comparative genomics techniques. It discusses three levels of genome research: structural genomics, functional genomics, and comparative genomics. Comparative genomics involves analyzing and comparing different genomes to study gene content, function, organization, and evolution. Techniques discussed include genome sequencing, mapping, and bioinformatics tools. The document also outlines what can be compared between genomes and how comparative genomics has provided insights into evolution and gene function.
Metagenomic
Metagenomics is the study of genomes recovered from environmental samples without culturing. It involves extracting DNA from an environmental sample and sequencing the DNA. This allows study of the 99% of microbes that cannot be cultured. Metagenomics has applications in discovering new antibiotics, enzymes, and understanding microbial communities and host interactions. It provides a culture-independent way to access genetic diversity and biotechnological potential from uncultured microorganisms.
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The document summarizes the sequencing of the yeast Saccharomyces cerevisiae genome. Key points:
1) The yeast genome was sequenced between 1989-1996 by over 35 European laboratories in a collaborative effort. By 1996, the entire 12 megabase genome across 16 chromosomes had been sequenced.
2) The genome contains approximately 6,000 open reading frames that were annotated after sequencing. About 30% of yeast genes have homologs in human genes.
3) Sequencing involved creating ordered cosmid libraries, shotgun sequencing, and assembling overlapping sequences into contigs. Genes were identified and analyzed after full genome assembly.
Sequence Submission Tools
In this presentation, I talk about the various tools for the submission of DNA or RNA sequences into various sequence databases. The sequence submission tools talked about in this presentation are BankIt, Sequin and Webin.
Fasta
FASTA is a bioinformatics tool and biological database that is used to compare amino acid sequences of proteins or nucleotide sequences of DNA. It was first described in 1985 by Lipman and Pearson. FASTA performs fast homology searches to find similarities between a query sequence and sequences in a database. While similar to BLAST, FASTA is faster for sequence comparisons. It works by identifying patches of sequence similarity that may contain gaps. Some key FASTA programs include FASTA, TFASTA, FASTS, and FASTX/Y. FASTA is useful for applications like identification of species, establishing phylogeny, DNA mapping, and understanding protein function.
Functional proteomics, and tools
INTRODUCTION HISTORY FUNCTIONAL PROTEOMICS PROTEOMICS SOFTWARE PROTEOME MAPPING TOOLS FOR PROTEOME ANALYSIS APPLICATIONS OF PROTEOMICS CONCLUSION REFERENCES
EMBL-EBI
The European Bioinformatics Institute (EBI) is a center for bioinformatics research and services located in Hinxton, UK. EBI grew out of EMBL's work providing public biological databases and offers major databases on DNA, RNA, proteins, pathways, and more. EBI's website provides access to these databases as well as a variety of bioinformatics tools for sequence analysis, proteomics, microarrays, and more through different channels on their site.
Genomics and bioinformatics
Genomics is the study of genomes and includes determining entire DNA sequences, genetic mapping, and studying intragenomic phenomena. It allows determining an ideal genotype. Genomics and bioinformatics provide benefits like improved crop productivity, stress tolerance, and nutritional quality. Proteomics studies proteins in cells. Bioinformatics handles large genomic and proteomic data using algorithms. Structural genomics constructs sequence data and maps genes. Functional genomics studies gene function. Comparative genomics compares sequences to find relationships.
Brief history and development of metagenomics
The document provides a brief history of metagenomics, beginning in the 17th century when Antonie van Leeuwenhoek first observed microbes using microscopes. Key developments included the definition of microbial communities, techniques for culturing microorganisms, and the realization that culture-based techniques did not capture total microbial diversity. The field of metagenomics emerged in the late 20th century with developments like PCR, sequencing of 16S rRNA, and shotgun sequencing of environmental samples without culturing. This led to insights into uncultured microbes and their roles in environments like acid mine drainage. Global metagenomic sampling projects helped discover thousands of new microbial species.
Next generation sequencing
This document summarizes a class seminar presentation on next generation sequencing technologies. It begins with an overview of DNA sequencing and its importance. It then reviews the history of sequencing technologies, from the discovery of DNA to the development of Sanger sequencing and next generation sequencing platforms. The document focuses on describing the Illumina/Solexa, 454, and SOLiD next generation sequencing methods. It explains the key steps in library preparation, cluster amplification, and sequencing by synthesis or ligation for these platforms. The advantages of next generation sequencing technologies over Sanger sequencing are also highlighted.
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental samples without culturing organisms. It allows researchers to study the 99.9% of microorganisms that cannot be cultured. Metagenomic analyses of ocean samples revealed over a million new genes and unexpected light-energy pathways in bacteria. Metagenomics has two main approaches - sequence-driven which sequences DNA and compares to databases, and function-driven which screens DNA clones for a desired function. Both approaches have limitations but are complementary. Metagenomics has applications in discovering new antibiotics and enzymes and studying human microbiomes and antibiotic resistance.
Functional genomics
This document discusses functional genomics and its approaches. It defines functional genomics as the worldwide experimental approach to access the function of genes by using information from structural genomics. The key functional genomics approaches discussed are transcriptomics, proteomics, metabolomics, interactomics, epigenetics, and nutrigenomics. Modern techniques discussed include expressed sequence tags (ESTs), serial analysis of gene expression (SAGE), and microarray analysis.
Est database
ESTs are short sequences of DNA that represent genes expressed in certain tissues or organisms. They provide a quick and inexpensive way for scientists to discover new genes and map their positions in genomes. ESTs represent a snapshot of genes expressed in a tissue at a given time. Sequencing the beginning or end of cDNA clones produces 5' and 3' ESTs, which can help identify genes and study gene expression and regulation.
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Structural genomics is a field that aims to determine the 3D structures of all proteins encoded by a genome. It involves determining structures on a large scale using techniques like X-ray crystallography and NMR. This allows identification of novel protein folds and potential drug targets. Comparative genomics compares genomic features between organisms and provides insights into evolution and conserved sequences and functions. It is a key tool in fields like medicine and agriculture.
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- The microbiome is established early in life and influenced by factors like birth method and antibiotic use in the first years. This early development can impact future health.
- Microbiome imbalances are linked to diseases like inflammatory bowel disease. New treatments are
Mathew's seminar
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Date: May 29, 2024
Tags: Information Security, ISO/IEC 27001, ISO/IEC 42001, Artificial Intelligence, GDPR
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Metagenomics analysis
- 1. Presented by G.Vijayalakshmi B.Sc.,M.Sc., 20PY10 Ayya Nadar Janaki Ammal college Sivakasi © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
- 2. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 What is Metagenomics? Traditional microbial genomics Sequence the genome of one organism at a time Use cultures to isolate microbe of interest Metagenomics Extract sequence data from microbial communities as they exist in nature Bypass the need for culture techniques Sequence all DNA in sample Select DNA based on universal sequences
- 3. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Techniques in Metagenomics Isolate DNA Depends on sample type Clone DNA Insert into plasmid Develop sample library Screen or sequence From Figure 2 in Daniel, R. (2005) "The Metagenomics of Soil" Nature Reviews Microbiology 3: 470-478.
- 4. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Analysis of Metagenomics Data Metagenomes are big Soil has as many as 40,000 individual microbial species Soil metagenome orders of magnitude bigger than human genome Analyzing the metagenome Screens Phylogenetic studies Sequencing uncultivated organisms Studying metagenome under different conditions
- 5. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Understanding Microbial Communities Some questions metagenomics may answer Are certain adaptations observable across environmental gradients? How do different species interact? Can lateral gene transfer be detected? From Figure 2 in Schleper, C., et al. (2005) "Genomics studies of uncultivated Archaea" Nature Reviews Microbiology 3: 479-488. Permission for figure 2 granted by K.Knittel and T.Loesekann,MPI Bremen, www.mumm-research.de.
- 6. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Applications $2.3 billion in sales of industrial enzymes in 2003 Discovery of novel enzymes and catalysts with industrial uses by screening thousands of microbial species simultaneously Look for pharmacologically interesting genes (e.g. antibiotics) that exist in organisms that cannot be cultured
- 7. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Caveats Problems with DNA purification Sample contamination Issues with sequencing Immensity of metagenome (gigabases) Errors in assembly due to inter-species similarities Difficulties in sequencing less well-represented genomes