EuKRef. A community effort towards phylogenetic-based curation of ribosomal databases for environmental sequencing

[13.07.07] karst mewe13 dna_extraction_nonotes

sorenkarst

This document discusses DNA extraction and primer selection for 16S amplicon sequencing of microbial communities. It recommends standardizing extraction protocols, using intense bead beating, and V1-3 primers for activated sludge samples. Experiments comparing different extraction parameters, storage conditions, and primers found that bead beating intensity and duration most affected community profiles in activated sludge. Standardizing protocols and selecting primers that maximize coverage are important for obtaining representative views of microbial ecology.

The OptIPlanet Collaboratory Supporting Microbial Metagenomics Researchers Wo...

The benefits of environment specific curation of the public databases for tax...

Aaron Marc Saunders

RefSoil ANL talk

Jinlyung Choi

This document outlines plans for multi-site sequencing studies to generate standardized human and bacterial genome sequencing datasets. Samples include a human trio, bacterial isolates, and mixtures, which will be sequenced in triplicate across three sites on various platforms including Illumina HiSeq X Ten, HiSeq 4000, HiSeq 2500, NextSeq 500, Life Tech Ion Proton, Ion S5, Pacific Biosciences, Oxford Nanopore, and others. The goals are to measure intra- and inter-lab variation, sequencing performance at GC extremes, and establish molecular standards for assessing sequencing methods in DNA, RNA, and metagenomics. Data will be analyzed by a team to benchmark tools and published by October 2017.

Big data nebraska

Adina Chuang Howe

The document discusses the rise of big data in microbiology due to decreasing costs of DNA sequencing and computational resources. It describes how high-throughput sequencing is generating vast amounts of microbial genomic and metagenomic data. However, analyzing these large, complex datasets presents numerous technical and social challenges for microbiologists, including handling data volume, integrating diverse data types, accessing resources, and incentivizing data sharing. Overcoming these bottlenecks will be key to unlocking the scientific insights contained within the microbial "big data" tidal wave.

[2013.10.29] albertsen genomics metagenomics

Mads Albertsen

This document provides an overview of genomics and metagenomics. It begins with an introduction to genomics, describing genome assembly, validation, and metabolic reconstruction. It then covers metagenomics, discussing its history, pitfalls, and potentials. Key points include that genomics analyzes the parts list of a single genome, while metagenomics analyzes the collective genomes of an entire microbial community. Metagenomics has been used to explore novel sequences from various environments, perform comparative analyses between ecosystems, and extract genomes from low-abundance species.

High-throughput sequencing and latent variable modelling of within-host paras...

Tuomas Aivelo

The document discusses using high-throughput DNA sequencing and statistical modeling to study parasite and microbiota communities within hosts. Large data sets on hundreds of host samples and thousands of species can identify within-host communities and determine how environmental and host variables affect composition. Statistical approaches allow modeling potential species interactions and generating testable hypotheses. Case studies of mouse lemurs and ticks demonstrate how longitudinal data collection reveals extensive within-individual variation in parasites and microbiota over time and across environments.

PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICS

Lubna MRL

After billions of years of evolution, prokaryotes have developed a huge diversity of regulatory mechanisms, many of which are probably uncharacterized. Now that the powerful tool of whole-transcriptome analysis can be used to study the RNA of bacteria and archaea, a new set of un expected RNA-based regulatory strategies might be revealed. Metagenomics, together with in vitro evolution and high-throughput screening technologies, provides industry with an unprecedented chance to bring biomolecules into industrial application.

Session 10: Building resilience in indigenous communities through engagement

Biosecurity issues impact on key crops and environmental values across NZ and Australia. A key outcome for the project team will be the ability of indigenous communities, and relevant regulatory authorities and industries, to better manage the social, environmental and economic impacts of biosecurity threats, and to participate in biosecurity strategies through improved bicultural engagement models that build empowerment and ownership in indigenous communities and their response to those threats. The teams have developed an engagement model adapted to the indigenous peoples and their communities of each country.

Science Seminar Series 4 Norman Johnson

University of Adelaide

The emerging biodiversity data ecosystem

Cyndy Parr

Schindel i evobio norman ok - jun 11

David Schindel

Session 2: Diagnostics in Africa

The Australia-Africa Plant Biosecurity Partnership has brought together plant biosecurity professionals in ten African countries and established linkages with Australian researchers, helping to reduce pest and disease impacts in sub-Saharan Africa. At the outset of this initiative, diagnostic skills were identified as a priority area in connecting Australian expertise with Africa and improving surveillance capability, post-entry quarantine, early warning and phytosanitary certification. This presentation will briefly examine the application of improved diagnostic skills in African Plant Protection Organisations and the longer term relationships that have been established with Australian mentors.

Session 6: New tools for field grains surveillance

amalthea_tr_2015_02

Kathryn Hollowood Jones

This document describes two methods for classifying frog calls using machine learning techniques: locality sensitive hashing (LSH) and Gaussian mixture modeling (GMM). For GMM classification, features are extracted from spectrograms of frog calls including filter responses and MFCC coefficients. Gaussian models are trained for each frog species using these features. Classification involves determining the most likely species model for a test call. Tests on 15 frog species showed promising 80% accuracy for GMM, approximating human performance. LSH classification was less accurate, suggesting noise and call variations limit its effectiveness.

Cross-Disciplinary Biomedical Research at Calit2

Session 10: Invasive fungus threatens Australian native communities

Myrtle rust (Puccinia psidii) is an invasive fungus native to South America that was first detected in Australia in 2010. It has spread rapidly along the east coast, and is currently recorded in sites as far north as the Northern Territory and south to Tasmania. In order to better understand myrtle rust extent and impacts in Australian native and managed landscapes, a survey was sent to national parks, botanical gardens, councils, natural resource managers, nurseries and forestry agencies in all states where the fungus is present (NT, QLD, NSW, VIC and TAS). The survey revealed that Myrtle rust is widespread in NSW and QLD gardens and streets as well as in native vegetation.

ABIcurator.doc

butest

This proposal requests $1.45 million from the NSF to develop a Curator Assistant to help communities annotate the rapidly increasing number of sequenced genomes. As sequencing costs decrease from $1 million to $10,000 per genome, the bottleneck has shifted to functional annotation, which currently relies on human curators. The proposed software will use natural language processing to extract gene functions from literature and suggest annotations to assist community curators with databases for non-model organisms lacking professional curation resources. It will initially focus on arthropod genomes through collaboration with the Arthropod Base Consortium.

2014 whitney-research

The document discusses challenges in analyzing non-model organism transcriptomics data due to lack of reference genomes and presents two solutions: digital normalization to reduce massive amounts of sequencing data while retaining important information, and partitioning transcripts into "transcript families" to collapse isoforms without a reference genome. It then provides examples of applying these approaches to lamprey and tunicate transcriptome data.

Bayesian Taxonomic Assignment for the Next-Generation Metagenomics

Extract 2.0: Text-mining-assisted interactive annotation

Lars Juhl Jensen

This document describes Extract 2.0, a text-mining tool that can assist with interactive annotation of documents. It uses dictionary-based tagging to identify relevant entities like genes and diseases. It achieves 70-80% recall and 80-90% precision on entity extraction and was evaluated in BioCreative challenges where it received positive feedback from curators. The tool is open source and available as a web service or Python wrapper.

2013 stamps-intro-assembly

C. Titus Brown is an assistant professor of microbiology and computer science at Michigan State University who focuses on analyzing and generating hypotheses from sequencing data. He gave a lecture on metagenome assembly. He discussed challenges with annotating individual short reads from environmental samples and emphasized the importance of assembly. He provided examples of successful metagenome assemblies including the genome reconstruction of symbionts from Osedax worms and tracking bacterial strains and phages in an infant gut microbiome over time. He outlined a "Grand Challenge" soil metagenomics project that aims to understand ecosystem functions and responses to perturbations through deep sequencing and assembly.

Phylotastic metagenomics

Holly Bik

Use of DNA barcoding and its role in the plant species/varietal Identifica...

Senthil Natesan

Plant DNA barcoding research is shifting beyond performance comparisons of different DNA regions towards practical applications. The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1(CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. The studies on cucumis sp for the application of DNA barcode shows the possibility of discrimination at species level not the varietal level using the matK gene barcode. The phylogenetic tree constructed by using matK gene sequences clearly differentiated the species C. sativus and C. melo which will help for the future application in cucumis taxonomy and phylogeny studies

What's hot

The Emerging Global Collaboratory for Microbial Metagenomics Researchers

Cross-Kingdom Standards in Genomics, Epigenomics and Metagenomics

Christopher Mason

Big data nebraska

Adina Chuang Howe

[2013.10.29] albertsen genomics metagenomics

Mads Albertsen

High-throughput sequencing and latent variable modelling of within-host paras...

Tuomas Aivelo

PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICS

Lubna MRL

Session 10: Building resilience in indigenous communities through engagement

Science Seminar Series 4 Norman Johnson

University of Adelaide

The emerging biodiversity data ecosystem

Cyndy Parr

Schindel i evobio norman ok - jun 11

David Schindel

Session 2: Diagnostics in Africa

Session 6: New tools for field grains surveillance

amalthea_tr_2015_02

Kathryn Hollowood Jones

Cross-Disciplinary Biomedical Research at Calit2

Session 10: Invasive fungus threatens Australian native communities

ABIcurator.doc

butest

2014 whitney-research

Bayesian Taxonomic Assignment for the Next-Generation Metagenomics

Extract 2.0: Text-mining-assisted interactive annotation

Lars Juhl Jensen

2013 stamps-intro-assembly

What's hot (20)

The Emerging Global Collaboratory for Microbial Metagenomics Researchers

Cross-Kingdom Standards in Genomics, Epigenomics and Metagenomics

Big data nebraska

[2013.10.29] albertsen genomics metagenomics

High-throughput sequencing and latent variable modelling of within-host paras...

PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICS

Session 10: Building resilience in indigenous communities through engagement

Science Seminar Series 4 Norman Johnson

The emerging biodiversity data ecosystem

Schindel i evobio norman ok - jun 11

Session 2: Diagnostics in Africa

Session 6: New tools for field grains surveillance

amalthea_tr_2015_02

Cross-Disciplinary Biomedical Research at Calit2

Session 10: Invasive fungus threatens Australian native communities

ABIcurator.doc

2014 whitney-research

Bayesian Taxonomic Assignment for the Next-Generation Metagenomics

Extract 2.0: Text-mining-assisted interactive annotation

2013 stamps-intro-assembly

Similar to EuKRef. A community effort towards phylogenetic-based curation of ribosomal databases for environmental sequencing

Phylotastic metagenomics

Holly Bik

Use of DNA barcoding and its role in the plant species/varietal Identifica...

Senthil Natesan

Bacterial Identification by 16s rRNA Sequencing.ppt

Rakesh Kumar

Bacteria are the most abundant life forms on Earth, with a single gram of soil containing 40 million bacterial cells. Most bacterial species have yet to be identified due to their abundance. DNA sequencing of the 16s rRNA gene is a common technique used to identify bacterial species. The process involves isolating bacteria from a sample, extracting DNA, amplifying and sequencing the 16s rRNA gene, and comparing the sequence to databases to identify matches. 16s rRNA gene sequencing provides a more accurate identification of bacteria than phenotypic methods.

Metagenomics

Surender Rawat

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.

Genome resource databases in horticutural crops

Pulipati Gangadhara Rao

This document discusses genomic resource conservation of horticultural crops. It defines genomic resources and describes the types that exist, including genomic, mitochondrial and chloroplast DNA, RNA, DNA markers, probes, primers, vectors, cloned genes, libraries, and sequence information. Genomic resources can be used for transgenic and cisgenic plant development, molecular breeding, germplasm screening, detailed understanding of plant biology, crop improvement through markers and genes, assessing diversity, and comparative genomics. The status of sequencing projects and EST resources available in public databases for various horticultural crops is presented. DNA banks that conserve genomic resources are described. Major plant DNA banks around the world are listed. Different genomic resource databases are provided. Future areas of focus include

Metagenomics

Chinthu V Saji

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.

Metagenomics

Jitesh Jaluthria

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.

iEvoBio Keynote: Frontiers of discovery with Encyclopedia of Life -- TRAITBANK

Cyndy Parr

16S classifier

Ashok Sharma

The diversity of microbial species in a metagenomic study is commonly assessed using 16S rRNA gene sequencing. With the rapid developments in genome sequencing technologies, the focus has shifted towards the sequencing of hypervariable regions of 16S rRNA gene instead of full length gene sequencing. Therefore, 16S Classifier is developed using a machine learning method, Random Forest, for faster and accurate taxonomic classification of short hypervariable regions of 16S rRNA sequence. It displayed precision values of up to 0.91 on training datasets and the precision values of up to 0.98 on the test dataset. On real metagenomic datasets, it showed up to 99.7% accuracy at the phylum level and up to 99.0% accuracy at the genus level. 16S Classifier is available freely at http://metagenomics.iiserb.ac.in/16Sclassifier and http://metabiosys.iiserb.ac.in/16Sclassifier.

Catalyzing Plant Science Research with RNA-seq

Manjappa Ganiger

RNA-seq is a revolutionary tool for transcriptomics that has advantages over previous methods like microarrays. It allows for single-base resolution expression profiling, detection of splicing variants and gene fusions, and can detect a wider dynamic range of expression levels. RNA-seq is being used to improve genome annotations by characterizing alternative splicing events and verifying gene boundaries. It is also useful for generating genetic resources for non-model species by performing de novo transcriptome sequencing and annotation. Additionally, RNA-seq can help advance proteomics by providing a reference database to match peptide spectra. Studies are using RNA-seq to examine spatial and temporal transcriptome landscapes in various plants.

Diversity Diversity Diversity Diversity ....

This document discusses the analysis of microbial communities through sequencing of the 16S rRNA gene. It presents WATERS, a workflow system that automates and bundles various software tools for analyzing 16S rRNA sequence data. The goals of WATERS are to simplify the analysis process for users without specialized bioinformatics expertise and to facilitate reproducibility through tracking of data provenance. WATERS guides users through the typical sequence analysis steps of alignment, chimera filtering, OTU clustering, taxonomy assignment, phylogeny tree building, and ecological analyses and visualization. By integrating existing tools into a single automated workflow, WATERS aims to reduce the effort required for 16S rRNA data analysis and allow researchers to focus on biological interpretation of results.

Global patterns of insect diiversity, distribution and evolutionary distinctness

Alison Specht

Metagenomics .pptx

MalikSahib22

Metagenomics , Applications, Techniques And Limitations .pptx

MalikSahib22

Kim Pruitt trainingbiocuration2015

Kim D. Pruitt

The document discusses curating sequence and literature data for RefSeq and Gene at the National Center for Biotechnology Information. It provides an overview of RefSeq, describing what RefSeq is, how it compares to GenBank, its advantages, and how the RefSeq dataset is built through curated data and sequence analysis. It then discusses the curation process in depth, including examples of curating genes, transcripts, proteins, and literature. It also describes the tools and quality assurance checks used in curation.

DNA AND RNA BASED TAXONOMY OF ANIMALS

abrishiya

This document discusses molecular taxonomy and DNA/RNA-based taxonomy of animals. Molecular techniques like DNA and protein sequencing, immunological methods, and DNA-DNA or DNA-RNA hybridization are used to establish genetic relationships between taxa and construct phylogenetic trees. DNA is extracted from specimens and specific genes are analyzed to find base sequences, which are then compared to standard sequences to identify species. RNA classification also helps with taxonomy, examining messenger RNA, ribosomal RNA, transfer RNA, and smaller nuclear RNA.

Next Generation Sequencing Technologies and Their Applications in Ornamental ...

Ravindra Kumar

This document summarizes research on DNA sequencing and genome sequencing techniques. It discusses early Sanger sequencing and the development of next-generation sequencing platforms like Roche 454, Illumina, Ion Torrent, and SOLiD. The document also presents two case studies, one on sequencing the carnation genome and another on obtaining the rose transcriptome to identify genes related to traits of interest. Overall, the document provides a high-level overview of the evolution of DNA sequencing technologies and their applications in sequencing plant genomes and transcriptomes.

Rapid Impact Assessment of Climatic and Physio-graphic Changes on Flagship G...

Arvinder Singh

Preeti singh12072017

Preeti Singh

This document discusses using information technology and bioinformatics to combine herbarium databases and leverage the information within them. It outlines developing tools to store, handle, and communicate herbarium data as databases grow massive in size from research. The goal is to provide digital access to herbarium collections for research and education. The method develops a universal XML format for herbarium data, uses Perl scripts to convert data, and an XPath query engine and Java applet for the user interface. Results demonstrate patterns in plant distributions and diversity to help conservation. Future directions include mapping tools, flexible queries, applications for different audiences, and integrating taxonomy and character databases.

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, a...