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Updated: Mar 21, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

Computational clustering for viral reference proteomes.

Chuming Chen¹, Hongzhan Huang¹, Raja Mazumder²

¹Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.

Bioinformatics (Oxford, England)

|May 7, 2016

Summary

This summary is machine-generated.

We introduce Viral Reference Proteomes (Viral RPs), a novel resource for analyzing viral proteins. These proteomes, clustered by protein similarity, aid in overcoming taxonomic challenges and facilitate functional annotation.

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Last Updated: Mar 21, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Published on: July 18, 2013

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

Area of Science:

Virology
Bioinformatics
Proteomics

Background:

Redundant sequenced genomes and undefined viral taxonomy complicate protein analysis.
Viral proteomes present unique challenges for functional annotation and classification.

Purpose of the Study:

To develop a normalized resource for viral proteomes to aid in functional annotation.
To address challenges posed by viral taxonomy and protein redundancy in genomic analysis.

Main Methods:

Computed Viral Reference Proteomes (Viral RPs) from complete virus proteomes in UniProtKB.
Generated Viral RPs using proteome similarity clusters at various co-membership thresholds (95%, 75%, 55%, 35%, 15%).
Compared computational Viral RPs with UniProt's curator-selected Reference Proteomes.

Main Results:

Developed Viral Reference Proteomes (Viral RPs) based on proteome similarity clustering.
Demonstrated consistency and complementarity between computational Viral RPs and UniProt's curated Reference Proteomes.
Showed that Viral RPs align with established virus or host taxonomy.

Conclusions:

Viral RPs provide a consistent and complementary resource for viral proteome analysis.
The developed Viral RPs facilitate functional annotation and overcome taxonomic ambiguities.
The resource is accessible via BLASTP search, FTP download, and a visualization browser.