scholarly journals Genome-Wide Covariation in SARS-CoV-2

2021 ◽  
Author(s):  
Evan Cresswell-Clay ◽  
Vipul Periwal
Keyword(s):  
Complete Genome ◽  
Open Reading Frames ◽  
Whole Genome ◽  
Genome Sequences ◽  
Direct Information ◽  
Global Pandemic ◽  
Genome Wide ◽  
A Genome ◽  
Encoded Proteins ◽  
Reading Frames

AbstractThe SARS-CoV-2 virus causing the global pandemic is a coronavirus with a genome of about 30Kbase length [Song et al., 2019]. The design of vaccines and choice of therapies depends on the structure and mutational stability of encoded proteins in the open reading frames(ORFs) of this genome. In this study, we computed, using Expectation Reflection, the genome-wide covariation of the SARS-CoV-2 genome based on an alignment of ≈ 130000 SARS-CoV-2 complete genome sequences obtained from GISAID[Shu & McCauley, 2017]. We used this covariation to compute the Direct Information between pairs of positions across the whole genome, investigating potentially important relationships within the genome, both within each encoded protein and between encoded proteins. We then computed the covariation within each clade of the virus. The covariation detected recapitulates all clade determinants and each clade exhibits distinct covarying pairs.

scholarly journals Genome Sequences of Two Dual-Serotype-Specific Echovirus 20 Strains from Nigeria

2019 ◽  
Vol 8 (43) ◽  
Author(s):  
T. O. C. Faleye ◽  
O. M. Adewumi ◽  
D. Klapsa ◽  
M. Majumdar ◽  
J. Martin ◽  
...  
Keyword(s):  
Amino Acids ◽  
Complete Genome ◽  
Neutralization Assay ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Here, we describe nearly complete genome sequences (7,361 nucleotides [nt] and 6,893 nt) of two echovirus 20 (E20) isolates from Nigeria that were simultaneously typed as CVB and E20 (dual serotype) by neutralization assay. Both include two overlapping open reading frames (ORFs) of 67 and 2,183 amino acids that encoded a recently described gut infection-facilitating protein and the classic enterovirus proteins, respectively.

scholarly journals Complete Genome Sequences of Pseudomonas aeruginosa Phages vB_PaeP_PcyII-10_P3P1 and vB_PaeM_PcyII-10_PII10A

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Christine Pourcel ◽  
Cédric Midoux ◽  
Libera Latino ◽  
Marie-Agnès Petit ◽  
Gilles Vergnaud
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Reading Frames

vB_PaeP_PcyII-10_P3P1 and vB_PaeM_PcyII-10_PII10A are Pseudomonas aeruginosa bacteriophages belonging, respectively, to the Lit1virus genus of the Podoviridae family and the Pbunavirus genus of the Myoviridae family. Their genomes are 72,778 bp and 65,712 bp long, containing 94 and 93 predicted open reading frames, respectively.

scholarly journals Coding-Complete Genome Sequences of an Iteradensovirus and an Alphapermutotetra-Like Virus Identified from the Pine Processionary Moth (Thaumetopoea pityocampa) in Portugal

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Franck Dorkeld ◽  
Réjane Streiff ◽  
Carole Kerdelhué ◽  
Mylène Ogliastro
Keyword(s):  
Complete Genome ◽  
Open Reading Frames ◽  
Thaumetopoea Pityocampa ◽  
Data Sets ◽  
Genome Sequences ◽  
Virus Family ◽  
Content Type ◽  
Pine Processionary Moth ◽  
Transcriptomic Data ◽  
Reading Frames

ABSTRACT The coding-complete genome sequences of an iteradensovirus (family Parvoviridae) and an alphapermutotetra-like virus (family Permutotetraviridae) were discovered from transcriptomic data sets obtained from Thaumetopoea pityocampa larvae collected in Portugal. Each of the coding-complete genome sequences of these viruses contains three main open reading frames (ORFs).

scholarly journals Complete Genome Sequence of Acinetobacter baumannii Phage BS46

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Anastasia V. Popova ◽  
Mikhail M. Shneider ◽  
Yulia V. Mikhailova ◽  
Andrey A. Shelenkov ◽  
Dmitry A. Shagin ◽  
...  
Keyword(s):  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Capsular Polysaccharides ◽  
Bacterial Host ◽  
Gene Encoding ◽  
Content Type ◽  
Double Stranded Dna ◽  
A Genome ◽  
Reading Frames

ABSTRACT Acinetobacter myovirus BS46 was isolated from sewage by J. S. Soothill in 1991. We have sequenced the genome of BS46 and found it to be almost unique. BS46 contains double-stranded DNA with a genome size of 94,068 bp and 176 predicted open reading frames. The gene encoding the tailspike that presumably possesses depolymerase activity toward the capsular polysaccharides of the bacterial host was identified.

scholarly journals Complete Genome Sequence of Pseudomonas aeruginosa Phage AAT-1

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Andrés Andrade-Domínguez ◽  
Roberto Kolter
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Medical Applications ◽  
Double Stranded Dna ◽  
A Genome ◽  
Reading Frames

Aspects of the interaction between phages and animals are of interest and importance for medical applications. Here, we report the genome sequence of the lytic Pseudomonas phage AAT-1, isolated from mammalian serum. AAT-1 is a double-stranded DNA phage, with a genome of 57,599 bp, containing 76 predicted open reading frames.

scholarly journals Complete Genome Sequence of a Bovine Ephemeral Fever Virus Isolate from Israel

2019 ◽  
Vol 8 (41) ◽  
Author(s):  
Daniel L. W. Dorey-Robinson ◽  
Mar Fernández de Marco ◽  
Luis M. Hernández-Triana ◽  
Arran J. Folly ◽  
Lorraine M. McElhinney ◽  
...  
Keyword(s):  
Complete Genome Sequence ◽  
Complete Genome ◽  
Virus Isolate ◽  
Genomic Sequence ◽  
Fever Virus ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Bovine Ephemeral Fever Virus ◽  
Bovine Ephemeral Fever ◽  
Reading Frames

Here, we report the first complete genome of a bovine ephemeral fever virus (BEFV) isolate from an infected bovine in Israel. The genome shares 95.3% identity with a Turkish genomic sequence but contains α3 and γ open reading frames that are truncated compared to those of existing BEFV genome sequences.

scholarly journals Complete Genome Sequence of a New Maize-Associated Cytorhabdovirus

2017 ◽  
Vol 5 (31) ◽  
Author(s):  
Kristen Willie ◽  
Lucy R. Stewart
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Nucleotide Sequence Identity ◽  
Open Reading Frames ◽  
Sequence Identity ◽  
Genome Wide ◽  
Maize Sample ◽  
Reading Frames

ABSTRACT A new 11,877-nucleotide cytorhabdovirus sequence with 6 open reading frames has been identified in a maize sample. It shares 50 and 51% genome-wide nucleotide sequence identity with northern cereal mosaic cytorhabdovirus and barley yellow striate mosaic cytorhabdovirus, respectively.

scholarly journals Genome Sequences of Ambystoma Tigrinum Virus Recovered during a Mass Die-off of Western Tiger Salamanders in Alberta, Canada

2019 ◽  
Vol 8 (29) ◽  
Author(s):  
Oliver Lung ◽  
Michelle Nebroski ◽  
Shivani Gupta ◽  
Cameron Goater
Keyword(s):  
Amino Acids ◽  
High Mortality ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Ambystoma Tigrinum ◽  
Genome Sequences ◽  
Ambystoma Tigrinum Virus ◽  
Content Type ◽  
Tiger Salamanders ◽  
Reading Frames

Complete genome sequences of six Ambystoma tigrinum viruses (ATV) were determined directly from tail clips of western tiger salamanders (Ambystoma mavortium) from 2013 (high-mortality year) and 2014 (low-mortality year) in Alberta, Canada. The genome lengths ranged from 106,258 to 106,915 bp and contained 108 open reading frames encoding predicted proteins larger than 50 amino acids.

scholarly journals Visualizing the periodic Ribo-seq reads with RiboPlotR

2019 ◽  
Author(s):  
Hsin-Yen Larry Wu ◽  
Polly Yingshan Hsu
Keyword(s):  
Mrna Translation ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Non Coding Rnas ◽  
Reading Frames ◽  
Small Open Reading Frames

ABSTRACTBackgroundRibo-seq has revolutionized the study of mRNA translation in a genome-wide scale. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes decipher three nucleotides each time. While the 3-nt periodicity has been widely used to study novel translation events and identify small open reading frames on presumed non-coding RNAs, tools which allow the visualization of those events remain underdeveloped.FindingsRiboPlotR is a visualization package written in R that presents both RNA-seq coverage and Ribo-seq reads for all annotated transcript isoforms in a context of a given gene. In particular, RiboPlotR plots Ribo-seq reads mapped in three reading frames using three colors for one isoform model at a time. Moreover, RiboPlotR shows Ribo-seq reads on upstream ORFs, 5’ and 3’ untranslated regions and introns, which is critical for observing new translation events and potential regulatory mechanisms.ConclusionsRiboPlotR is freely available (https://github.com/hsinyenwu/RiboPlotR) and allows the visualization of the translating features in Ribo-seq data.

scholarly journals Genome Sequences of Two Marsupial Simplex Viruses, Macropodid Alphaherpesviruses 2 and 4

2021 ◽  
Vol 10 (2) ◽  
Author(s):  
P. K. Vaz ◽  
T. J. Mahony ◽  
C. A. Hartley ◽  
J. Motha ◽  
J. M. Devlin
Keyword(s):  
Open Reading Frames ◽  
Nucleotide Identity ◽  
Diagnostic Tools ◽  
Genome Sequences ◽  
Genome Wide ◽  
Marsupial Species ◽  
Reading Frames

ABSTRACT We present the genome sequences of macropodid alphaherpesviruses 2 and 4, two closely related pathogens of macropods. Both encoded 68 nonredundant open reading frames (ORFs) and share 90.6% genome-wide nucleotide identity. These viruses are associated with fatal outbreaks of disease in multiple marsupial species. These sequences will be important for the development of new diagnostic tools.

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