scholarly journals Releasing the Kraken

2021 ◽  
Vol 1 ◽  
Author(s):  
Steven L. Salzberg ◽  
Derrick E. Wood
Keyword(s):  
Inflection Point ◽  
Standard Technique ◽  
Microbial Genomes ◽  
Microbiome Analysis ◽  
Comprehensive Database ◽  
Analysis Tools ◽  
Dramatic Rise

Ten years ago, the dramatic rise in the number of microbial genomes led to an inflection point, when the approach of finding short, exact matches in a comprehensive database became just as accurate as older, slower approaches. The new idea led to a method that was hundreds of times times faster than those that came before. Today, exact k-mer matching is a standard technique at the heart of many microbiome analysis tools.

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 The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community

2021 ◽  
Vol 12 ◽  
Author(s):  
Zeynep Koşaloğlu-Yalçın ◽  
Nina Blazeska ◽  
Hannah Carter ◽  
Morten Nielsen ◽  
Ezra Cohen ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Epitope Prediction ◽  
Target Prediction ◽  
Sequencing Data ◽  
Related Data ◽  
Prediction Tools ◽  
Comprehensive Collection ◽  
Analysis Tools ◽  
Dramatic Rise

Recent years have witnessed a dramatic rise in interest towards cancer epitopes in general and particularly neoepitopes, antigens that are encoded by somatic mutations that arise as a consequence of tumorigenesis. There is also an interest in the specific T cell and B cell receptors recognizing these epitopes, as they have therapeutic applications. They can also aid in basic studies to infer the specificity of T cells or B cells characterized in bulk and single-cell sequencing data. The resurgence of interest in T cell and B cell epitopes emphasizes the need to catalog all cancer epitope-related data linked to the biological, immunological, and clinical contexts, and most importantly, making this information freely available to the scientific community in a user-friendly format. In parallel, there is also a need to develop resources for epitope prediction and analysis tools that provide researchers access to predictive strategies and provide objective evaluations of their performance. For example, such tools should enable researchers to identify epitopes that can be effectively used for immunotherapy or in defining biomarkers to predict the outcome of checkpoint blockade therapies. We present here a detailed vision, blueprint, and work plan for the development of a new resource, the Cancer Epitope Database and Analysis Resource (CEDAR). CEDAR will provide a freely accessible, comprehensive collection of cancer epitope and receptor data curated from the literature and provide easily accessible epitope and T cell/B cell target prediction and analysis tools. The curated cancer epitope data will provide a transparent benchmark dataset that can be used to assess how well prediction tools perform and to develop new prediction tools relevant to the cancer research community.

scholarly journals OperonDB: a comprehensive database of predicted operons in microbial genomes

2009 ◽  
Vol 37 (Database) ◽  
pp. D479-D482 ◽  
Author(s):  
M. Pertea ◽  
K. Ayanbule ◽  
M. Smedinghoff ◽  
S. L. Salzberg
Keyword(s):  
Microbial Genomes ◽  
Comprehensive Database

The Analysis of Dislocations Using a Symmetry Criterion

1972 ◽  
Vol 30 ◽  
pp. 660-661
Author(s):  
J. C. Ingram ◽  
P. R. Strutt ◽  
Wen-Shian Tzeng
Keyword(s):  
Electron Beam ◽  
Electron Microscope ◽  
Displacement Field ◽  
Standard Technique ◽  
Residual Image ◽  
Symmetry Criterion

The invisibility criterion which is the standard technique for determining the nature of dislocations seen in the electron microscope can at times lead to erroneous results or at best cause confusion in many cases since the dislocation can still show a residual image if the term is non-zero, or if the edge and screw displacements are anisotropically coupled, or if the dislocation has a mixed character. The symmetry criterion discussed below can be used in conjunction with and in some cases supersede the invisibility criterion for obtaining a valid determination of the nature of the dislocation.The symmetry criterion is based upon the well-known fact that a dislocation, because of the symmetric nature of its displacement field, can show a symmetric image when the dislocation is correctly oriented with respect to the electron beam.

Stereo imaging in the shadow electron microscope

1978 ◽  
Vol 36 (1) ◽  
pp. 120-121
Author(s):  
W. C. T. Dowell
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Convenient Method ◽  
Patent Application ◽  
Standard Technique ◽  
Stereo Imaging ◽  
Stereo Images ◽  
Specimen Height

Stereo imaging is not new to electron microscopy. Von Ardenne, who first published transmission pairs nearly forty hears ago, himself refers to a patent application by Ruska in 1934. In the early days of the electron microscope von Ardenne employed a pair of magnetic lenses to view untilted specimens but soon opted for the now standard technique of tilting the specimen with respect to the beam.In the shadow electron microscope stereo images can, of course, be obtained by tilting the specimen between micrographs. This obvious method suffers from the disadvantage that the magnification is very sensitive to small changes in specimen height which accompany tilting in the less sophisticated stages and it is also time consuming. A more convenient method is provided by horizontally displacing the specimen between micrographs. The specimen is not tilted and the technique is both simple and rapid, stereo pairs being obtained in less than thirty seconds.

Finding decision support requirements for effective intelligence analysis tools

2005 ◽  
Author(s):  
William Elm ◽  
Scott Potter ◽  
James Tittle ◽  
David Woods ◽  
Justin Grossman ◽  
...  
Keyword(s):  
Decision Support ◽  
Intelligence Analysis ◽  
Analysis Tools

Construction of Author-based Corpus and Development of Analysis Tools

2018 ◽  
Vol 56 ◽  
pp. 235-254
Author(s):  
Hyeon-Yeol Im
Keyword(s):  
Analysis Tools

Credit Market Depth and Income Inequality in Vietnam: A Panel-Data Analysis

2016 ◽  
pp. 5-18
Author(s):  
Hoi Le Quoc ◽  
Hoi Chu Minh
Keyword(s):  
Data Analysis ◽  
Panel Data ◽  
Income Inequality ◽  
Financial Development ◽  
Inflection Point ◽  
Panel Data Analysis ◽  
Credit Market ◽  
Method Of Moment ◽  
Market Depth ◽  
Generalized Method Of Moment

Financial development could exert various effects on income distribution of a country. By employing Generalized Method of Moment, this paper aims at examining the impacts of credit market depth, one of most used financial development barometers, on income inequality in Vietnam. The empirical findings show that expanding credit market in the country could lead to higher income inequality. We have not found evidence that supports the hypothesis of an inverted U-shaped relation ever introduced by Greenwood and Jovanovich, although this hypothesis may still hold in a sense that Vietnam has not reached to the inflection point to generate such a curve alike.

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