scholarly journals Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation

2020 ◽  
Author(s):  
Michael J. Tisza ◽  
Anna K. Belford ◽  
Guillermo Dominguez-Huerta ◽  
Benjamin Bolduc ◽  
Matthew B. Sullivan ◽  
...  
Keyword(s):  
High Performance ◽  
Hypothetical Protein ◽  
Virus Discovery ◽  
Great Abundance ◽  
User Input ◽  
Genome Maps ◽  
Highly Sensitive ◽  
Viral Sequences ◽  
Gene Information ◽  
High Performance Computation

AbstractViruses, despite their great abundance and significance in biological systems, remain largely mysterious. Indeed, the vast majority of the perhaps hundreds of millions of viral species on the planet remain undiscovered. Additionally, many viruses deposited in central databases like GenBank and RefSeq are littered with genes annotated as “hypothetical protein” or the equivalent. Cenote-Taker2, a virus discovery and annotation tool available on command line and with a graphical user interface with free high-performance computation access, utilizes highly sensitive models of hallmark virus genes to discover familiar or divergent viral sequences from user-input contigs. Additionally, Cenote-Taker2 uses a flexible set of modules to automatically annotate the sequence features of contigs, providing more gene information than comparable tools. The outputs include readable and interactive genome maps, virome summary tables, and files that can be directly submitted to GenBank. We expect Cenote-Taker2 to facilitate virus discovery, annotation, and expansion of the known virome.

scholarly journals Cenote-Taker 2 Democratizes Virus Discovery And Sequence Annotation

2020 ◽  
Author(s):  
Michael J Tisza ◽  
Anna K Belford ◽  
Guillermo Dominguez-Huerta ◽  
Benjamin Bolduc ◽  
Christopher B Buck
Keyword(s):  
High Performance ◽  
Hypothetical Protein ◽  
Virus Discovery ◽  
Great Abundance ◽  
User Input ◽  
Genome Maps ◽  
Highly Sensitive ◽  
Viral Sequences ◽  
Gene Information ◽  
High Performance Computation

Abstract Viruses, despite their great abundance and significance in biological systems, remain largely mysterious. Indeed, the vast majority of the perhaps hundreds of millions of viral species on the planet remain undiscovered. Additionally, many viruses deposited in central databases like GenBank and RefSeq are littered with genes annotated as “hypothetical protein” or the equivalent. Cenote-Taker 2, a virus discovery and annotation tool available on command line and with a graphical user interface with free high-performance computation access, utilizes highly sensitive models of hallmark virus genes to discover familiar or divergent viral sequences from user-input contigs. Additionally, Cenote-Taker 2 uses a flexible set of modules to automatically annotate the sequence features of contigs, providing more gene information than comparable tools. The outputs include readable and interactive genome maps, virome summary tables, and files that can be directly submitted to GenBank. We expect Cenote-Taker 2 to facilitate virus discovery, annotation, and expansion of the known virome.

Ultraviolet light-emitting diode-assisted highly sensitive room temperature NO2 gas sensor for low-temperature solution-processed ZnO/TiO2 nanorods decorated with plasmonic Au nanoparticles

Nanoscale ◽  
2021 ◽  
Author(s):  
Soon-Hwan Kwon ◽  
Tae-Hyeon Kim ◽  
Sang-Min Kim ◽  
Semi Oh ◽  
Kyoung-Kook Kim
Keyword(s):  
Gas Sensors ◽  
High Performance ◽  
Room Temperature ◽  
Au Nanoparticles ◽  
Light Emitting Diode ◽  
Light Emitting ◽  
No2 Gas Sensor ◽  
Highly Sensitive ◽  
Temperature Solution ◽  
Semiconducting Metal Oxides

Nanostructured semiconducting metal oxides such as SnO2, ZnO, TiO2, and CuO have been widely used to fabricate high performance gas sensors. To improve the sensitivity and stability of gas sensors,...

A rapid and highly sensitive method for simultaneous determination of bioactive constituents in leaf extracts of six Ocimum species using ultra high performance liquid chromatography-hybrid linear ion trap triple quadrupole mass spectrometry

2016 ◽  
Vol 8 (2) ◽  
pp. 333-341 ◽  
Author(s):  
Renu Pandey ◽  
Preeti Chandra ◽  
Brijesh Kumar ◽  
Bhupender Dutt ◽  
Kulwant Rai Sharma
Keyword(s):  
Food Processing ◽  
High Performance ◽  
Ion Trap ◽  
Linear Ion Trap ◽  
Quadrupole Mass ◽  
Bioactive Constituents ◽  
Leaf Extracts ◽  
Highly Sensitive ◽  
Ocimum Species

Ocimum species have tremendous value in pharmaceutical, perfumery, food processing and cosmetic industries, also in traditional rituals and medicines.

scholarly journals The virome of German bats: comparing virus discovery approaches

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Claudia Kohl ◽  
Annika Brinkmann ◽  
Aleksandar Radonić ◽  
Piotr Wojtek Dabrowski ◽  
Kristin Mühldorfer ◽  
...  
Keyword(s):  
Virus Detection ◽  
Detection Methods ◽  
Single Type ◽  
Metagenomic Sequencing ◽  
Virus Discovery ◽  
Highly Pathogenic ◽  
Pcr Screening ◽  
Specific Pcr ◽  
Pathogenic Viruses ◽  
Viral Sequences

AbstractBats are known to be reservoirs of several highly pathogenic viruses. Hence, the interest in bat virus discovery has been increasing rapidly over the last decade. So far, most studies have focused on a single type of virus detection method, either PCR, virus isolation or virome sequencing. Here we present a comprehensive approach in virus discovery, using all three discovery methods on samples from the same bats. By family-specific PCR screening we found sequences of paramyxoviruses, adenoviruses, herpesviruses and one coronavirus. By cell culture we isolated a novel bat adenovirus and bat orthoreovirus. Virome sequencing revealed viral sequences of ten different virus families and orders: three bat nairoviruses, three phenuiviruses, one orbivirus, one rotavirus, one orthoreovirus, one mononegavirus, five parvoviruses, seven picornaviruses, three retroviruses, one totivirus and two thymoviruses were discovered. Of all viruses identified by family-specific PCR in the original samples, none was found by metagenomic sequencing. Vice versa, none of the viruses found by the metagenomic virome approach was detected by family-specific PCRs targeting the same family. The discrepancy of detected viruses by different detection approaches suggests that a combined approach using different detection methods is necessary for virus discovery studies.

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