MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes DOI Creative Commons
Clément Coclet, Antônio Pedro Camargo, Simon Roux

et al.

mSystems, Journal Year: 2024, Volume and Issue: 9(10)

Published: Oct. 1, 2024

ABSTRACT While numerous computational frameworks and workflows are available for recovering prokaryote eukaryote genomes from metagenome data, only a limited number of pipelines designed specifically viromics analysis. With many tools developed in the last few years alone, it can be challenging scientists with bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, calculate relative abundance coverage viral using state-of-the-art methods standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, user-friendly pipeline written Python providing simple framework perform standard analyses. MVP combines multiple enable genome identification, characterization filtering, clustering, taxonomic functional annotation, binning, comprehensive summaries results that used downstream ecological Overall, provides standardized reproducible both extensive robust viruses large-scale sequencing data including metagenomes, metatranscriptomes, viromes, isolate genomes. As typical use case, show how entire applied set 20 metagenomes wetland sediments 10 modules executed via command lines, leading identification 11,656 contigs 8,145 operational units (vOTUs) displaying clear beta-diversity pattern. Further, acting as dynamic wrapper, is continuously incorporate updates integrate new tools, ensuring its ongoing relevance rapidly evolving field viromics. at https://gitlab.com/ccoclet/mvp versioned packages PyPi Conda. IMPORTANCE The significance our work lies development (MVP), an integrated tailored exclusively stands out due modular design, which ensures easy installation, execution, integration databases. By combining such geNomad CheckV, high-quality recovery taxonomy host assignment, addressing limitations existing pipelines. MVP’s ability handle diverse sample types, environmental, human microbiome, plant-associated samples, makes versatile tool broader microbiome research community. standardizing analysis process interpretable results, enables researchers studies communities, significantly advancing understanding ecology impact on various ecosystems.

Language: Английский

Advances in artificial intelligence-envisioned technologies for protein and nucleic acid research DOI Creative Commons
Amol D. Gholap, Abdelwahab Omri

Drug Discovery Today, Journal Year: 2025, Volume and Issue: unknown, P. 104362 - 104362

Published: April 1, 2025

Artificial intelligence (AI) and machine learning (ML) have revolutionized pharmaceutical research, particularly in protein nucleic acid studies. This review summarizes the current status of AI ML applications sector, focusing on innovative tools, web servers, databases. paper highlights how these technologies address key challenges drug development including high costs, lengthy timelines, complexity biological systems. Furthermore, potential personalized medicine, cancer response prediction, biomarker identification is discussed. The integration research promises to accelerate discovery, reduce ultimately lead more effective therapeutic strategies.

Language: Английский

Citations

0
Multiomic Insights into Human Health: Gut Microbiomes of Hunter-Gatherer, Agropastoral, and Western Urban Populations DOI Creative Commons
Harinder Singh, Rosana Wiscovitch-Russo,

Claire Kuelbs

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 4, 2024

Societies with exposure to preindustrial diets exhibit improved markers of health. Our study used a comprehensive multi-omic approach reveal that the gut microbiome Ju/'hoansi hunter-gatherers, one most remote KhoeSan groups, higher diversity and richness, an abundance microbial species lost in western population. The showed enhanced global transcription enrichment complex carbohydrate metabolic energy generation pathways. also show high short-chain fatty acids are associated health optimal immune function. In contrast, these pathways their respective were found low or completely absent Western populations. Amino acid metabolism observed prevalent population, biomarkers chronic inflammation. provides first in-depth characterization microbiome, revealing uncharacterized functional

Language: Английский

Citations

0
MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes DOI Creative Commons
Clément Coclet, Antônio Pedro Camargo, Simon Roux

et al.

mSystems, Journal Year: 2024, Volume and Issue: 9(10)

Published: Oct. 1, 2024

ABSTRACT While numerous computational frameworks and workflows are available for recovering prokaryote eukaryote genomes from metagenome data, only a limited number of pipelines designed specifically viromics analysis. With many tools developed in the last few years alone, it can be challenging scientists with bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, calculate relative abundance coverage viral using state-of-the-art methods standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, user-friendly pipeline written Python providing simple framework perform standard analyses. MVP combines multiple enable genome identification, characterization filtering, clustering, taxonomic functional annotation, binning, comprehensive summaries results that used downstream ecological Overall, provides standardized reproducible both extensive robust viruses large-scale sequencing data including metagenomes, metatranscriptomes, viromes, isolate genomes. As typical use case, show how entire applied set 20 metagenomes wetland sediments 10 modules executed via command lines, leading identification 11,656 contigs 8,145 operational units (vOTUs) displaying clear beta-diversity pattern. Further, acting as dynamic wrapper, is continuously incorporate updates integrate new tools, ensuring its ongoing relevance rapidly evolving field viromics. at https://gitlab.com/ccoclet/mvp versioned packages PyPi Conda. IMPORTANCE The significance our work lies development (MVP), an integrated tailored exclusively stands out due modular design, which ensures easy installation, execution, integration databases. By combining such geNomad CheckV, high-quality recovery taxonomy host assignment, addressing limitations existing pipelines. MVP’s ability handle diverse sample types, environmental, human microbiome, plant-associated samples, makes versatile tool broader microbiome research community. standardizing analysis process interpretable results, enables researchers studies communities, significantly advancing understanding ecology impact on various ecosystems.

Language: Английский

Citations

0