Search engine for discovering works of Art, research articles, and books related to Art and Culture
Javascript must be enabled to continue!
Computational methods for the discovery and annotation of viral integrations
View through CrossRef
Abstract
The transfer of genetic material between viruses and eukaryotic cells is pervasive. Somatic integrations of DNA viruses and retroviruses have been linked to persistent viral infection and genotoxic effects. Integrations into germline cells, referred to as Endogenous Viral Elements (EVEs), can be co-opted for host functions. Besides DNA viruses and retroviruses, EVEs can also derive from nonretroviral RNA viruses, which have often been observed in piRNA clusters. Here, we describe a bioinformatic framework to annotate EVEs in a genome assembly, study their widespread occurrence and polymorphism and identify sample-specific viral integrations using whole-genome sequencing data.
Title: Computational methods for the discovery and annotation of viral integrations
Description:
Abstract
The transfer of genetic material between viruses and eukaryotic cells is pervasive.
Somatic integrations of DNA viruses and retroviruses have been linked to persistent viral infection and genotoxic effects.
Integrations into germline cells, referred to as Endogenous Viral Elements (EVEs), can be co-opted for host functions.
Besides DNA viruses and retroviruses, EVEs can also derive from nonretroviral RNA viruses, which have often been observed in piRNA clusters.
Here, we describe a bioinformatic framework to annotate EVEs in a genome assembly, study their widespread occurrence and polymorphism and identify sample-specific viral integrations using whole-genome sequencing data.
Related Results
Viral Hijacking of Host RNA-Binding Proteins: Implications for Viral Replication and Pathogenesis
Viral Hijacking of Host RNA-Binding Proteins: Implications for Viral Replication and Pathogenesis
In the intricate dance between viruses and host cells, RNA-binding proteins (RBPs) serve as crucial orchestrators of gene expression and cellular processes. We will delve into the ...
Bioinformatics analysis and collection of protein post-translational modification sites in human viruses
Bioinformatics analysis and collection of protein post-translational modification sites in human viruses
AbstractIn viruses, post-translational modifications (PTMs) are essential for their life cycle. Recognizing viral PTMs is very important for better understanding the mechanism of v...
An extensible genome annotation workbench based on the Galaxy Platform
An extensible genome annotation workbench based on the Galaxy Platform
Introduction
Falling costs of genetic sequencing have allowed sequencing and annotation of the genomes of non-model organism. In annotating non-mod...
Benchmarking Hayai-Annotation Plants: A Re-evaluation Using Standard Evaluation Metrics
Benchmarking Hayai-Annotation Plants: A Re-evaluation Using Standard Evaluation Metrics
Abstract
The rapid growth of next-generation sequencing (NGS) technology has led to a surge in the determination of whole genome sequences in pla...
Comparative analysis of gene prediction tools for viral genome annotation
Comparative analysis of gene prediction tools for viral genome annotation
Abstract
The number of newly available viral genomes and metagenomes has increased exponentially since the development of high throughput sequencing platforms and g...
FAMUS: A Few-Shot Learning Framework for Large-Scale Protein Annotation
FAMUS: A Few-Shot Learning Framework for Large-Scale Protein Annotation
Predicting gene function is a pivotal and challenging step in genomic and metagenomic data analysis. Current automatic annotation tools typically rely on the single most similar se...
Human Immunodeficiency Virus Viral Load Monitoring and Rate of Virologic Suppression Among Patients Receiving Antiretroviral Therapy in Democratic Republic of the Congo, 2013–2020
Human Immunodeficiency Virus Viral Load Monitoring and Rate of Virologic Suppression Among Patients Receiving Antiretroviral Therapy in Democratic Republic of the Congo, 2013–2020
Abstract
Background
Antiretroviral therapy (ART) expansion and viral load as a treatment monitoring approach have increased the ...
Hepatitis B Virus Integration into Transcriptionally Active Loci and HBV-Associated Hepatocellular Carcinoma
Hepatitis B Virus Integration into Transcriptionally Active Loci and HBV-Associated Hepatocellular Carcinoma
Hepatitis B Virus (HBV) DNA integrations into the human genome are considered major causative factors to HBV-associated hepatocellular carcinoma development. In the present study, ...