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Related Concept Videos

Human Virome01:26

Human Virome

The human body harbors a vast and diverse viral community known as the human virome. The virome includes bacteriophages that infect bacteria, and eukaryotic viruses that infect human cells. Transient dietary and environmental viruses also contribute to this dynamic ecosystem. Estimates suggest the human body may contain on the order of 10¹³ viral particles, though abundance varies widely by body site and detection method.Comprehensive characterization of the virome has become possible only with...
Viruses with RNA Genomes01:29

Viruses with RNA Genomes

RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
Viral Structure00:56

Viral Structure

Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.
Subviral Agents01:29

Subviral Agents

Subviral agents are infectious entities that resemble viruses but lack one or more viral components, such as a capsid or essential replication machinery. These agents include viroids, prions, and satellites, each possessing distinct structural and functional characteristics that influence their mode of infection and replication.Viroids are the simplest subviral agents, consisting of circular, single-stranded RNA molecules without a protein coat. They exclusively infect plants, relying entirely...
The Antiviral System of Bacteria and Archaea: CRISPR01:23

The Antiviral System of Bacteria and Archaea: CRISPR

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats is a adaptive immune system found in bacteria and archaea that protects against viral infections. This system enables prokaryotic cells to identify, remember, and neutralize foreign genetic elements, primarily bacteriophages, by storing fragments of the invader’s DNA as a genetic memory.The CRISPR immune response begins during an initial infection. Cas (CRISPR-associated) proteins play a central role in this defense.

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In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions
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CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and

Ivan Borozan1, Shane Wilson, Paola Blanchette

  • 1Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada.

BMC Bioinformatics
|August 21, 2012
PubMed
Summary
This summary is machine-generated.

A new bioinformatics platform, CaPSID, aids in detecting infectious agents in cancer genomes. This tool enhances pathogen discovery and analysis in tumor sequencing data, improving cancer research.

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Area of Science:

  • Oncology
  • Bioinformatics
  • Infectious Disease

Background:

  • Approximately 20% of human cancers are linked to infectious agents.
  • The discovery of novel oncogenic pathogens is crucial for understanding cancer etiology.
  • Next-generation sequencing technologies offer opportunities for pathogen detection in tumors.

Purpose of the Study:

  • To introduce CaPSID, a bioinformatics platform for pathogen sequence identification in tumor genomes and transcriptomes.
  • To provide a tool for querying and visualizing both exogenous and endogenous pathogen sequences.
  • To develop efficient genome-wide bioinformatics tools for pathogen discovery.

Main Methods:

  • CaPSID is a comprehensive bioinformatics platform for pathogen sequence identification.
  • It features a scalable database and integrates the JBrowse genome browser.
  • The platform analyzes pre-aligned BAM files, offering metrics like gene and genome coverage.

Main Results:

  • CaPSID successfully identified all human and pathogen sequences in a simulated dataset.
  • Analysis of ovarian cancer transcriptome samples demonstrated CaPSID's efficiency.
  • Predictions made by CaPSID were validated in vitro.

Conclusions:

  • CaPSID is a useful and efficient tool for pathogen detection in cancer research.
  • The platform facilitates the identification and analysis of oncogenic pathogens.
  • CaPSID contributes to advancing the understanding of infectious agents in cancer.