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95 results for “Viral genome”
All-atom models of SU10 and P68 viral genomes. Supplementary to the "Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses".
<p>The dataset contains mmCIF formatted all-atom models of SU10 and P68 viral genomes and the python script used for refinement of the initial MMB-generated coordinates.</p>
Viral reference genomes to disentangle the recombinant phylogenetic history of the potyviruses
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Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features"
<p>Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features" (submitted to Nature Communications)</p>
Datasets - Unveiling Host-Parasite Relationships through Conserved MITEs in Prokaryote and Viral Genomes
<p><em><span>Title:</span></em></p> <p><strong><span>Unveiling Host-Parasite Relationships through Conserved MITEs in Prokaryote and Viral Genomes<span> </span></span></strong></p> <p><em><span> </span></em></p> <p><em><span>Authors:</span></em></p> <p><span>Francisco Nadal-Molero<sup>(1)</sup>, Riccardo Roselli<sup>(1)</sup>, Silvia Garcia-Juan<sup>(1)</sup>, Alicia Campos-Lopez<sup>(1)</sup>, Ana-Belen Martin-Cuadrado<sup>(1*)</sup></span></p> <p> </p> <p><strong><span>SUPPLEMENTARY FILES</span></strong></p> <p><strong><span> </span></strong></p> <p><strong><span>Supplementary File S1.</span></strong><span> Sequences of cMITEs detected in Bacteria genomes (<em>fasta</em> format). The hosting microbial species and inferred NCBI-taxonomy are indicated in the name of each sequence. The structure of the MITE name is: “Accession|Genome|start|end|TSD|TIRlength|MITETracker_group|Lineage”.</span></p> <p><strong><span>Supplementary File S2.</span></strong><span> Sequences of cMITEs detected in the Archaea genomes (<em>fasta</em> format). The hosting microbial species and inferred NCBI-taxonomy are indicated in the name of each sequence. The structure of the MITE name is: “Accession|Genome|start|end|TSD|TIRlength|MITETracker_group|Lineage”.</span></p> <p><strong><span>Supplementary File S3.</span></strong><span> Sequences of vMITEs detected in the virus sequences from the NCBI and IMG/VR v.4.1 database (<em>fasta</em> format). Virus, microbial host (if known) and inferred NCBI-taxonomy is stated in the name of each sequence. The structure of the MITE name is: </span></p> <p><span>“Accession|Genome|start|end|TSD|TIRlength|MITETracker_group|Virus|Name|Host”.</span></p> <p><strong><span>Supplementary File S4.</span></strong><span> Sequences of <span>si-vMITEs</span> detected in the virus sequences from the NCBI and IMG/VR v.4.1 database (<em>fasta</em> format). Virus, microbial host (if known) and inferred NCBI-taxonomy are stated in the name of each sequence. The structure of the MITE name is: “Accession|Genome|start|end|Ident.Method.by.DB|Host”.</span></p> <p><strong><span>Supplementary Files S5. </span></strong><span>Cytoscape networks. (A) Figure 1A, (B) Figure 1B.</span></p> <p><strong><span>Supplementary File S6.</span></strong><span> Sequences of cMITEs obtained from <span>5837</span> genomes of Neisseriales. The structure of the MITE name is: </span></p> <p><span>“Accession|NucleotideID|start|end|TSD|TIRlength|MITETracker_group|Genome|Lineage”.</span></p> <p><strong><span>Supplementary File S7.</span></strong><span> Sequences of si-vMITEs obtained from <span>5837</span> genomes of Neisseriales. The structure of the MITE name is: “Accession|Genome|start|end|Host”.</span></p> <p><strong><span>Supplementary File S8.</span></strong><span> Sequences of cMITEs obtained from 46051 genomes of Bacteroidota. The structure of the MITE name is:</span></p> <p><span>“Accession|NucleotideID|start|end|TSD|TIRlength|MITETracker_group|Genome|Lineage”.</span></p> <p><strong><span>Supplementary File S9.</span></strong><span> Sequences of si-vMITEs obtained from 46051 genomes of Bacteroidota. The structure of the MITE name is: “Accession|Genome|start|end|Host”.</span></p>
Ancient viral genomes reveal introduction of HBV and B19V into Mexico during the transatlantic slave trade
<p>After the European colonization of the Americas there was a dramatic population collapse of the Indigenous inhabitants caused in part by the introduction of new pathogens. Although there is much speculation on the etiology of the Colonial epidemics, direct evidence for the presence of specific viruses during the Colonial era is lacking. To uncover the diversity of viral pathogens during this period, we designed an enrichment assay targeting ancient DNA (aDNA) from viruses of clinical importance and applied it on DNA extracts from individuals found in a Colonial hospital and a Colonial chapel (16th c. – 18th c.) where records suggest victims of epidemics were buried during important outbreaks in Mexico City. This allowed us to reconstruct three ancient human parvovirus B19 genomes, and one ancient human hepatitis B virus genome from distinct individuals. The viral genomes are similar to African strains, consistent with the inferred morphological and genetic African ancestry of the hosts as well as with the isotopic analysis of the human remains, suggesting an origin on the African continent. This study provides direct molecular evidence of ancient viruses being transported to the Americas during the transatlantic slave trade and their subsequent introduction to New Spain. Altogether, our observations enrich the discussion about the etiology of infectious diseases during the Colonial period in Mexico.</p>
Simulated viral genomes dataset (TargetCall-D5)
<p>Detailed description:</p> <p>The fast5 files in this dataset is generated using Deep Simulator for 7 different viral genomes.</p> <p>This dataset includes 35K fast5 files in total.</p>
Viral genomes, functional genes, and microbial genomes of 144 activated sludge samples taken from 54 WWTPs across 13 countries on a global scale
<p>The study dataset contains 85,114 viral genomes, 1,115,185 viral functional genes, and 3,823 microbial genomes obtained from 54 WWTPs across 13 countries. </p><p>If this study dataset is useful, please cite: Fan, X., Ji, M., Mu, D. <i>et al.</i> Global diversity and biogeography of DNA viral communities in activated sludge systems. <i>Microbiome</i> <strong>11</strong>, 234 (2023). https://doi.org/10.1186/s40168-023-01672-1</p>
Enhancing Protein Sequence Annotation in Viral Genomics Using Large Language Models and Soft Alignments.
<p>List of 200 most abundant VOG descriptions.</p>
Ancient viral genomes reveal introduction of HBV and B19V into Mexico during the transatlantic slave trade
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Genomic and immunogenic changes of Piscine novirhabdovirus (Viral hemorrhagic septicemia virus) over its evolutionary history in the Laurentian Great Lakes
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Data from: Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.
Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found dominant among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes concludes to the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the Microvirus. In addition, a peptidase gene was found in 11 Microviridae and its analysis concludes to a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in microviruses. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.
Healthy woodchuck genome with viral sequences appended used for single-cell RNA-seq analysis
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Data from: Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.
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Data from: Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
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Data from: Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
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Nuclear Lamina binds the EBV genome during latency and regulates viral gene expression [RNA-seq]
GEO Series GSE181012. Homo sapiens; human gammaherpesvirus 4. 10 samples. Type: Expression profiling by high throughput sequencing.
Defective Epstein-Barr Virus Genomes and Atypical Viral Gene Expression in B-Cell Lines Derived from Multiple Myeloma Patients [III]
GEO Series GSE171494. Homo sapiens. 2 samples. Type: Other.
Applying defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs
GEO Series GSE180632. Severe acute respiratory syndrome coronavirus 2. 3 samples. Type: Expression profiling by high throughput sequencing.
m6A sequencing of HIV viral genomic RNA and infected host cell samples
GEO Series GSE85724. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Defective Epstein-Barr Virus Genomes and Atypical Viral Gene Expression in B-Cell Lines Derived from Multiple Myeloma Patients [I]
GEO Series GSE165194. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.