scholarly journals ReferenceSeeker: rapid determination of appropriate reference genomes

2020 ◽  
Vol 5 (46) ◽  
pp. 1994
Author(s):  
Oliver Schwengers ◽  
Torsten Hain ◽  
Trinad Chakraborty ◽  
Alexander Goesmann
Keyword(s):  
Rapid Determination ◽  
Reference Genomes

scholarly journals ReferenceSeeker: rapid determination of appropriate reference genomes

2019 ◽  
Author(s):  
O. Schwengers ◽  
T. Hain ◽  
T. Chakraborty ◽  
A. Goesmann
Keyword(s):  
Rapid Determination ◽  
Single Nucleotide ◽  
Microbial Genomes ◽  
Polymorphism Detection ◽  
Command Line Tool ◽  
Subsequent Calculation ◽  
In Silico Analyses ◽  
Reference Genomes ◽  
Selection Of

AbstractSummaryThe large and growing number of microbial genomes available in public databases makes the optimal selection of reference genomes necessary for many in-silico analyses, e.g. single nucleotide polymorphism detection, scaffolding and comparative genomics, increasingly difficult. Here, we present ReferenceSeeker, a novel command line tool combining a fast kmer profile-based database lookup of candidate reference genomes with subsequent calculation of highly specific average nucleotide identity (ANI) values for the rapid determination of appropriate reference genomes. Pre-built databases for bacteria, archaea, fungi, protozoa and viruses based on the RefSeq database are provided for download.Availability and ImplementationReferenceSeeker is open source software implemented in Python. Source code and binaries are freely available for download at https://github.com/oschwengers/referenceseeker under the GNU GPL3 [email protected]

Weak Beam Imaging and Diffraction Studies of Stacking Faults in Silicon

1976 ◽  
Vol 34 ◽  
pp. 590-591
Author(s):  
T. Y. Tan ◽  
W. K. Tice
Keyword(s):  
Fast Neutron ◽  
Rapid Determination ◽  
Stacking Faults ◽  
Imaging Method ◽  
Large Reduction ◽  
Dislocation Loops ◽  
Fringe Spacing ◽  
Weak Beam ◽  
Kinematical Theory

In studying ion implanted semiconductors and fast neutron irradiated metals, the need for characterizing small dislocation loops having diameters of a few hundred angstrom units usually arises. The weak beam imaging method is a powerful technique for analyzing these loops. Because of the large reduction in stacking fault (SF) fringe spacing at large sg, this method allows for a rapid determination of whether the loop is faulted, and, hence, whether it is a perfect or a Frank partial loop. This method was first used by Bicknell to image small faulted loops in boron implanted silicon. He explained the fringe spacing by kinematical theory, i.e., ≃l/(Sg) in the fault fringe in depth oscillation. The fault image contrast formation mechanism is, however, really more complicated.

Methods for rapid determination of pecan (Carya illinoensis) seed viability

2017 ◽  
Vol 45 (2) ◽  
pp. 455-464
Author(s):  
T.T. Xue ◽  
J. Liu ◽  
Y.B. Shen ◽  
G.Q. Liu
Keyword(s):  
Rapid Determination ◽  
Seed Viability ◽  
Carya Illinoensis
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