scholarly journals UNIVERSAL LENGTHS IN COMPLETE MICROBIAL GENOMES

2004 ◽  
Vol 18 (17n19) ◽  
pp. 2448-2454 ◽  
Author(s):  
T. Y. CHEN ◽  
L. C. HSIEH ◽  
C. H. CHANG ◽  
L. F. LUO ◽  
F. M. JI ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Rna World ◽  
Initial Length ◽  
Microbial Genomes ◽  
Complete Genomes ◽  
Frequency Occurrence

Statistical analysis of frequency occurrence of short words in complete genomes reveals the existence of a set of universal lengths common to all extant complete microbial genomes. This phenomenon is consistent with a model for genome growth in which primitive genomes grew mainly by maximally stochastic duplications of short segments from an initial length of about 200 nucleotides. The relevance of these results to the so-called RNA world in which life began and evolved before the rise of proteins is discussed.

scholarly journals The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes

2019 ◽  
Author(s):  
Maria A. Sierra ◽  
Chandrima Bhattacharya ◽  
Krista Ryon ◽  
Sophie Meierovich ◽  
Heba Shaaban ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Gram Stain ◽  
Microbial Genomes ◽  
Resistance To Antibiotics ◽  
Microbial Species ◽  
Gene Annotations ◽  
Comprehensive Database ◽  
Broad Community

AbstractThe Microbe Directory (TMD) is a comprehensive database of annotations for microbial species collating features such as gram-stain, capsid-symmetry, resistance to antibiotics and more. This work presents a significant improvement to the original Microbe Directory (2018). This update adds 68,852 taxa, many new annotation features, an interface for the statistical analysis of microbiomes based on TMD features, and presents a portal for the broad community to add or correct entries. This update also adds curated lists of gene annotations which are useful for characterizing microbial genomes. Much of the new data in TMD is sourced from a set of databases and independent studies collating these data into a single quality controlled and curated source. This will allow researchers and clinicians to have easier access to microbial data and provide for the possibility of serendipitous discovery of otherwise unexpected trends.

scholarly journals Complete microbial genomes for public health in Australia and Southwest Pacific

2019 ◽  
Author(s):  
Sarah L. Baines ◽  
Anders Gonçalves da Silva ◽  
Glen Carter ◽  
Amy V. Jennison ◽  
Irani Rathnayake ◽  
...  
Keyword(s):  
Public Health ◽  
Microbial Pathogens ◽  
Whole Genome Sequence ◽  
Concerted Effort ◽  
Microbial Genomes ◽  
Southwest Pacific ◽  
Complete Genomes ◽  
Phylogenomic Analyses ◽  
Regional Public Health ◽  
Pathogen Strains

AbstractComplete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.AnnouncementWhole-genome sequence (WGS) data is increasingly important in public health microbiology (1–4). The data can be used to replicate many of the basic bacterial sub-typing approaches, as well as support epidemiological investigations, such as surveillance and outbreak investigation (5–7). The appeal of WGS data comes from the promise of a single workflow to process all microbial pathogens that can provide easily portable data that promotes deeper integration of surveillance and investigation efforts across jurisdictions. This promise is leading to a concerted effort to move microbial public health to a primarily genome-based workflow at numerous jurisdictions (8–10), including Australia (11).

scholarly journals The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities

2020 ◽  
Vol 49 (D1) ◽  
pp. D751-D763 ◽  
Author(s):  
I-Min A Chen ◽  
Ken Chu ◽  
Krishnaveni Palaniappan ◽  
Anna Ratner ◽  
Jinghua Huang ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
User Interface ◽  
Data Management ◽  
Protein Family ◽  
Joint Genome Institute ◽  
Annotation Pipeline ◽  
Microbial Genomes ◽  
Advanced Search ◽  
Analysis System

Abstract The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) contains annotated isolate genome and metagenome datasets sequenced at the DOE’s Joint Genome Institute (JGI), submitted by external users, or imported from public sources such as NCBI. IMG v 6.0 includes advanced search functions and a new tool for statistical analysis of mixed sets of genomes and metagenome bins. The new IMG web user interface also has a new Help page with additional documentation and webinar tutorials to help users better understand how to use various IMG functions and tools for their research. New datasets have been processed with the prokaryotic annotation pipeline v.5, which includes extended protein family assignments.

scholarly journals Complete microbial genomes for public health in Australia and the Southwest Pacific

2020 ◽  
Vol 6 (12) ◽  
Author(s):  
Sarah L. Baines ◽  
Anders Gonçalves da Silva ◽  
Glen P. Carter ◽  
Amy Jennison ◽  
Irani Rathnayake ◽  
...  
Keyword(s):  
Public Health ◽  
Pathogenic Bacteria ◽  
Microbial Pathogens ◽  
Bacterial Genomes ◽  
High Quality ◽  
Microbial Genomes ◽  
Southwest Pacific ◽  
Complete Genomes ◽  
Phylogenomic Analyses ◽  
Regional Public Health

Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific; enriching the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health microbiology laboratories. In this first step, we present 26 complete high-quality bacterial genomes. Additionally, we describe here a framework for reconstructing complete microbial genomes and highlight some of the challenges and considerations for accurate and reproducible genome reconstruction.

Statistical analysis of classification

1966 ◽  
Vol 24 ◽  
pp. 188-189
Author(s):  
T. J. Deeming
Keyword(s):  
Multivariate Analysis ◽  
Statistical Analysis ◽  
Classification Scheme ◽  
Analytical Procedure ◽  
Narrow Band ◽  
Scientific Research ◽  
Maximum Amount ◽  
Amount Of Information

If we make a set of measurements, such as narrow-band or multicolour photo-electric measurements, which are designed to improve a scheme of classification, and in particular if they are designed to extend the number of dimensions of classification, i.e. the number of classification parameters, then some important problems of analytical procedure arise. First, it is important not to reproduce the errors of the classification scheme which we are trying to improve. Second, when trying to extend the number of dimensions of classification we have little or nothing with which to test the validity of the new parameters.Problems similar to these have occurred in other areas of scientific research (notably psychology and education) and the branch of Statistics called Multivariate Analysis has been developed to deal with them. The techniques of this subject are largely unknown to astronomers, but, if carefully applied, they should at the very least ensure that the astronomer gets the maximum amount of information out of his data and does not waste his time looking for information which is not there. More optimistically, these techniques are potentially capable of indicating the number of classification parameters necessary and giving specific formulas for computing them, as well as pinpointing those particular measurements which are most crucial for determining the classification parameters.

Quantitative parallel EELS spectrum imaging developed as a new tool in AEM

1992 ◽  
Vol 50 (2) ◽  
pp. 1202-1203
Author(s):  
Gianluigi Botton ◽  
Gilles L'espérance
Keyword(s):  
Statistical Analysis ◽  
Spatial Resolution ◽  
Personal Computer ◽  
Systematic Study ◽  
Present Author ◽  
Chemical Elements ◽  
Detection Limits ◽  
Research Groups ◽  
Quantitative Performance ◽  
Spectrum Imaging

As interest for parallel EELS spectrum imaging grows in laboratories equipped with commercial spectrometers, different approaches were used in recent years by a few research groups in the development of the technique of spectrum imaging as reported in the literature. Either by controlling, with a personal computer both the microsope and the spectrometer or using more powerful workstations interfaced to conventional multichannel analysers with commercially available programs to control the microscope and the spectrometer, spectrum images can now be obtained. Work on the limits of the technique, in terms of the quantitative performance was reported, however, by the present author where a systematic study of artifacts detection limits, statistical errors as a function of desired spatial resolution and range of chemical elements to be studied in a map was carried out The aim of the present paper is to show an application of quantitative parallel EELS spectrum imaging where statistical analysis is performed at each pixel and interpretation is carried out using criteria established from the statistical analysis and variations in composition are analyzed with the help of information retreived from t/γ maps so that artifacts are avoided.

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