Computational clustering for viral reference proteomes

The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome s...

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Bibliographic Details
Published in:Bioinformatics 2016-07, Vol.32 (13), p.2041-2043
Main Authors: Chen, Chuming, Huang, Hongzhan, Mazumder, Raja, Natale, Darren A, McGarvey, Peter B, Zhang, Jian, Polson, Shawn W, Wang, Yuqi, Wu, Cathy H
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Applications Notes
Bioinformatics
Cluster Analysis
Clusters
Computation
Computational Biology
Databases, Protein
Knowledge Bases
Proteins
Proteome - analysis
Searching
Similarity
Taxonomy
Viral Proteins - analysis
Viruses
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Summary:The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies. We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95, 75, 55, 35 and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt's curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs. http://proteininformationresource.org/rps/viruses/ chenc@udel.edu Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btw110