{"doi":"10.1093/bioinformatics/btw110","title":"Computational clustering for viral reference proteomes","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Motivation: 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.</jats:p>\n               <jats:p>Results: 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.</jats:p>\n               <jats:p>Availability and implementation:  http://proteininformationresource.org/rps/viruses/</jats:p>\n               <jats:p>Contact:  chenc@udel.edu</jats:p>\n               <jats:p>Supplementary information:  Supplementary data are available at Bioinformatics online.</jats:p>","journal":"Bioinformatics","year":2016,"id":20460,"datarank":0.4672049991996532,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.22578931233453814,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.22578931233453814,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":3,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":135148,"name":"Hongzhan Huang","orcid":null,"position":1,"is_corresponding":false},{"id":57231,"name":"Raja Mazumder","orcid":"0000-0001-8823-9945","position":2,"is_corresponding":false},{"id":57228,"name":"Darren A. Natale","orcid":"0000-0001-5809-9523","position":3,"is_corresponding":false},{"id":135149,"name":"Peter B. McGarvey","orcid":null,"position":4,"is_corresponding":false},{"id":27403,"name":"Jian Zhang","orcid":"0000-0002-8824-8574","position":5,"is_corresponding":false},{"id":123406,"name":"Shawn W. Polson","orcid":null,"position":6,"is_corresponding":false},{"id":135150,"name":"Yuqi Wang","orcid":null,"position":7,"is_corresponding":false},{"id":118770,"name":"Cathy H. Wu","orcid":null,"position":8,"is_corresponding":false},{"id":135147,"name":"Chuming Chen","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"27153712","pmcid":"PMC4920120","openalex_id":"https://openalex.org/W2288906059","authors":[],"funders":[],"total_grants":0,"fwci":0.3091,"citation_percentile":0.67854088,"influential_citations":0,"citation_trend":[{"year":2018,"count":1},{"year":2022,"count":3}],"oa_status":"bronze","license":null,"oa_locations":[{"url":"https://academic.oup.com/bioinformatics/article-pdf/32/13/2041/16920728/btw110.pdf","host_type":"journal"},{"url":"https://doi.org/10.1093/bioinformatics/btw110","host_type":"BRONZE"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/32/13/2041/16920728/btw110.pdf","host_type":"publisher"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/32/13/2041/49019832/bioinformatics_32_13_2041.pdf","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/27153712","host_type":"repository"},{"url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/13/2041","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4920120","host_type":"repository"}],"fields_of_study":["Bacteriophages and microbial interactions","vaccines and immunoinformatics approaches","Advanced Proteomics Techniques and Applications","Computer Science","Biology","Medicine","Amino Acid Sequence","Cluster Analysis","Computational Biology","Databases, Protein","Knowledge Bases","Proteome","Viral Proteins"],"mesh_terms":["Amino Acid Sequence","Viral Proteins","Cluster Analysis","Computational Biology","Proteome","Databases, Protein","Knowledge Bases"],"keywords":["UniProt","Proteome","Computational biology","Biology","Genome","Cluster analysis","Bioinformatics","Computer science","Genetics","Artificial intelligence"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-04T15:03:53.160521Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}