Origins and challenges of viral dark matter.

Krishnamurthy SR; Wang D

doi:10.1016/j.virusres.2017.02.002

Origins and challenges of viral dark matter.

Krishnamurthy SR ¹,

Wang D ¹

Affiliations

1. Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Authors
Krishnamurthy SR¹
Wang D¹
(2 authors)

ORCIDs linked to this article

Krishnamurthy SR | 0000-0003-1777-8292

Virus Research, 09 Feb 2017, 239:136-142
https://doi.org/10.1016/j.virusres.2017.02.002 PMID: 28192164

Review

Abstract

The accurate classification of viral dark matter - metagenomic sequences that originate from viruses but do not align to any reference virus sequences - is one of the major obstacles in comprehensively defining the virome. Depending on the sample, viral dark matter can make up from anywhere between 40 and 90% of sequences. This review focuses on the specific nature of dark matter as it relates to viral sequences. We identify three factors that contribute to the existence of viral dark matter: the divergence and length of virus sequences, the limitations of alignment based classification, and limited representation of viruses in reference sequence databases. We then discuss current methods that have been developed to at least partially circumvent these limitations and thereby reduce the extent of viral dark matter.

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https://en.wikipedia.org/wiki/Biological_dark_matter

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Origins and challenges of viral dark matter.

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Authors

ORCIDs linked to this article

Abstract

Full text links

References

Basic local alignment search tool.

The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication.

Characterization of a novel orthomyxo-like virus causing mass die-Offs of tilapia

A measure of the similarity of sets of sequences not requiring sequence alignment.

Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs.

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.

Fast and sensitive protein alignment using DIAMOND

CpG usage in RNA viruses: data and hypotheses.

Virus attenuation by genome-scale changes in codon pair bias

Analysis of double-stranded RNA from microbial communities identifies double-stranded RNA virus-like elements.

Citations & impact

Impact metrics

Citations of article over time

Alternative metrics

Article citations

Findings and methodologies in oral phageome research: a systematic review.

Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.

Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter.

VOGDB-Database of Virus Orthologous Groups.

Predicting novel mosquito-associated viruses from metatranscriptomic dark matter.

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Wikipedia

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Author information

Affiliations

Authors

ORCIDs linked to this article

Abstract

Full text links

References

Characterization of a novel orthomyxo-like virus causing mass die-Offs of tilapia

Fast and sensitive protein alignment using DIAMOND

Virus attenuation by genome-scale changes in codon pair bias

Citations & impact

Impact metrics

Citations of article over time

Alternative metrics

Article citations

Other citations

Wikipedia

Similar Articles

Partnerships & funding