A5040654425- Invertebrate Taxonomy and Ecology
- Genomics and Phylogenetic Studies
- Species Distribution and Climate Change
- Mediterranean and Iberian flora and fauna
- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Biological Control of Invasive Species
- Plant Pathogens and Fungal Diseases
- Identification and Quantification in Food
- Marine Biology and Ecology Research
- Nematode management and characterization studies
- Diatoms and Algae Research
- Plant and Fungal Species Descriptions
- Microbial Metabolism and Applications
- Parasite Biology and Host Interactions
- Aquaculture disease management and microbiota
- Plant Pathogenic Bacteria Studies
- Microbial Natural Products and Biosynthesis
- Plant and animal studies
- Plant Disease Resistance and Genetics
- Probiotics and Fermented Foods
- Bacteriophages and microbial interactions
- Algal biology and biofuel production
- Enzyme Production and Characterization
- Legume Nitrogen Fixing Symbiosis
Michigan State University
2014-2024
NamesforLife (United States)
2013-2022
Wellcome Centre for Mitochondrial Research
2018
University of Newcastle Australia
2018
Newcastle University
2018
Michigan United
2011-2014
Botanic Garden and Botanical Museum Berlin
2011
Freie Universität Berlin
2011
Michigan Public Health Institute
2011
UK Centre for Ecology & Hydrology
2010
ABSTRACT The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. majority classifications (98%) were high estimated (≥95%) accuracy (98%). In addition...
The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality faster processing of user sequences. Substantial new features include Pyrosequencing Pipeline that tools support ultra high-throughput sequencing data. This pipeline offers collection automate data simplify...
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide...
An ad hoc committee for the re-evaluation of species definition in bacteriology met Gent, Belgium, February 2002. The made various recommendations regarding light developments methodologies available to systematists.
The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along analysis services a phylogenetically consistent taxonomic framework for these data.Updated monthly, are made available through RDP-II website (http:// rdp.cme.msu.edu/).RDP-II release 9.21 (August 2004) contains 101 632 bacterial small subunit sequences in format.Highthroughput tools initial placement, identification of related probe primer testing, data navigation...
The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences the research community. Through its website ( http://rdp.cme.msu.edu ), RDP-II offers aligned annotated rRNA sequence analysis services, phylogenetic inferences (trees) derived from these data. release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, 1503 mitochondrial small subunit in format. current public beta of 9.0 debuts a new regularly updated alignment over 50 000...
The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173–174], continued during the past year to add new rRNA sequences aligned data and improve analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 prokaryotic small subunit (SSU) while number eukaryotic mitochondrial SSU in form remained at 2055 1503, respectively. more than doubled from previous release 14 months earlier, ~75% are longer 899 bp. An RDP-II mirror site...
Substantial new features have been implemented at the Ribosomal Database Project in response to increased importance of high-throughput rRNA sequence analysis microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available sequences introduction myRDP Space, a web component designed help researchers place their own data context with RDP's data. In addition, video tutorials describe how use RDP features. Details...
The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (1997), 25, 109–111], is now hosted the Center for Microbial Ecology at Michigan State University. RDP-II a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, associated computer programs. During past two years, alignments have been updated include >9700 small subunit rRNA sequences. recent development of an ObjectStore...
We here present annotated lists of names Candidatus taxa prokaryotes with ranks between subspecies and class, proposed the mid-1990s, when provisional status was first established, end 2018. Where necessary, corrected are that comply current provisions International Code Nomenclature Prokaryotes its Orthography appendix. These lists, as well updated newly published additions corrections to be periodically in Journal Systematic Evolutionary Microbiology, may serve basis for valid publication...
The purpose of this announcement is to effect the valid publication following effectively published new names and combinations under procedure described in Bacteriological Code (1990 Revision). Authors other individuals wishing have and/or included future lists should send three copies pertinent reprint or photocopies thereof, an electronic copy paper IJSEM Editorial Office for confirmation that all requirements been met. It also a requirement ICSP authors species, subspecies provide...
After the International Committee on Systematics of Prokaryotes (ICSP) had voted to include rank phylum in rules Code Nomenclature (ICNP), and following publication decision IJSEM, we here present names formal descriptions 42 phyla effect valid their names, based genera as nomenclatural types.
This volume contains the edition of International Code Nomenclature Prokaryotes that was presented in draft form and available for comment at Plenary Session Fourteenth Congress Bacteriology Applied Microbiology (BAM), Montréal, 2014, together with updated lists conserved rejected bacterial names Opinions issued by Judicial Commission. As past it brings those changes accepted, published documented ICSP Commission since last revision published. Several new appendices have been added to this...
The methodologies used to generate genome and metagenome annotations are diverse vary between groups laboratories. Descriptions of the annotation process helpful in interpreting data. Some have produced Standard Operating Procedures (SOPs) that describe process, but standards lacking for structure content these descriptions. In addition, there is no central repository store disseminate procedures protocols annotation. We highlight importance SOPs endorse an online SOPs.
More detailed sequence standards that keep up with revolutionary sequencing technologies will aid the research community in evaluating data.
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher we support invest in the microbiology community, to benefit of everyone. This supports our principal goal develop, expand strengthen networks available members so that they can generate new knowledge about microbes ensure it is shared with other communities.
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher we support invest in the microbiology community, to benefit of everyone. This supports our principal goal develop, expand strengthen networks available members so that they can generate new knowledge about microbes ensure it is shared with other communities.
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher we support invest in the microbiology community, to benefit of everyone. This supports our principal goal develop, expand strengthen networks available members so that they can generate new knowledge about microbes ensure it is shared with other communities.
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher we support invest in the microbiology community, to benefit of everyone. This supports our principal goal develop, expand strengthen networks available members so that they can generate new knowledge about microbes ensure it is shared with other communities.
In recent decades, the taxonomy of Bacteria and Archaea , therefore genus designation, has been largely based on use a single ribosomal gene, 16S rRNA as taxonomic marker. We propose an approach to delineate genera that excludes direct gene focuses standard genome relatedness index, average nucleotide identity. Our findings are importance microbiology community because emergent properties identified in this study will help assign with higher resolution.
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher we support invest in the microbiology community, to benefit of everyone. This supports our principal goal develop, expand strengthen networks available members so that they can generate new knowledge about microbes ensure it is shared with other communities.