A PHP Error was encountered

Severity: Warning

Message: fopen(/var/lib/php/sessions/ci_session8i5p5gduc87tl142q0t2nfa8q1b8t2ca): Failed to open stream: No space left on device

Filename: drivers/Session_files_driver.php

Line Number: 177

Backtrace:

File: /var/www/html/index.php
Line: 316
Function: require_once

A PHP Error was encountered

Severity: Warning

Message: session_start(): Failed to read session data: user (path: /var/lib/php/sessions)

Filename: Session/Session.php

Line Number: 137

Backtrace:

File: /var/www/html/index.php
Line: 316
Function: require_once

VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation. | LitMetric

VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation.

Bioinformatics

Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China SAR.

Published: October 2024

AI Article Synopsis

  • * VirTAXA is a new tool that helps classify RNA viruses at the genus level using advanced methods like remote homology search and tree-based validation.
  • * This tool improves upon existing methods by accurately assigning genus labels to more viral sequences; it can also be adapted for use with other virus types.

Article Abstract

Summary: RNA viruses are ubiquitous across a broad spectrum of ecosystems. Therefore, beyond their significant implications for public health, RNA viruses are also key players in ecological processes. High-through sequencing has accelerated the discovery of RNA viruses. Nevertheless, many of these viruses lack taxonomic annotation, posing a challenge to functional inference and evolutionary study. In particular, virus classification at the genus level remains difficult due to the limited reference data and ambiguous boundaries between some closely related genera. We introduce VirTAXA, a robust classification tool that combines remote homology search and tree-based validation to enhance the genus-level taxonomic classification of RNA viruses. VirTAXA is able to predict the genus label of an assembled viral contig and provide evidence type for each prediction. It achieves comparable accuracy to state-of-the-art methods while assigning genus labels to a greater number of sequences. Specifically, on the Global Ocean RNA metatranscriptomic data, VirTAXA can assign genus labels for 18% more contigs than the second-best classification tool. Furthermore, we demonstrated that VirTAXA can be conveniently extended to other types of viruses.

Availability And Implementation: The source code and data of VirTAXA are available via https://github.com/JudithEllyn/VirTAXA.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11464415PMC
http://dx.doi.org/10.1093/bioinformatics/btae575DOI Listing

Publication Analysis

Top Keywords

rna viruses
16
taxonomic classification
8
remote homology
8
homology search
8
search tree-based
8
tree-based validation
8
classification tool
8
genus labels
8
data virtaxa
8
virtaxa
6

Similar Publications

Background: is a transmitted respiratory pathogen that causes high morbidity and mortality in children, especially those under 5 years of age. During the implementation of population control measures for COVID-19 in mainland China, the detection rate in pediatric patients decreased. However, with the second wave of the COVID-19 pandemic (2022), the incidence of pneumococcal disease (PD) and even invasive pneumococcal disease (IPD) began to rise again.

View Article and Find Full Text PDF

Unraveling the impact of SARS-CoV-2 mutations on immunity: insights from innate immune recognition to antibody and T cell responses.

Front Immunol

December 2024

Laboratory of Molecular Medicine, Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.

Throughout the COVID-19 pandemic, the emergence of new viral variants has challenged public health efforts, often evading antibody responses generated by infections and vaccinations. This immune escape has led to waves of breakthrough infections, raising questions about the efficacy and durability of immune protection. Here we focus on the impact of SARS-CoV-2 Delta and Omicron spike mutations on ACE-2 receptor binding, protein stability, and immune response evasion.

View Article and Find Full Text PDF

The functional specialization of CD4 T lymphocytes into various subtypes, including T1 and T cells, is crucial for effective immune responses. T cells facilitate B cell differentiation within germinal centers, while T1 cells are vital for cell-mediated immunity against intracellular pathogens. Integrin α4, a cell surface adhesion molecule, plays significant roles in cell migration and co-stimulatory signaling.

View Article and Find Full Text PDF

Coronavirus disease 2019 (COVID-19) is a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2. Nasopharyngeal swabs (NP swabs) were used for patients with COVID-19 who demonstrated serious clinical symptoms and disturbances in biochemical parameters. The biochemical profiles of these patients remain ambiguous and differ from wave to wave of COVID-19 infections.

View Article and Find Full Text PDF

Introduction: following the detection of vaccine-derived poliovirus in 2019 in Ethiopia, response activities have been conducted including strengthening disease surveillance activities.

Methods: trend analysis study design of acute flaccid paralysis and measles surveillance data for the years 2021 and 2022 for Southwest Ethiopia Region was used. The non-polio acute flaccid paralysis (AFP) rate and stool adequacy rates were used to assess the AFP surveillance.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!