{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T09:45:52Z","timestamp":1753868752543,"version":"3.41.2"},"reference-count":45,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2024,6,10]],"date-time":"2024-06-10T00:00:00Z","timestamp":1717977600000},"content-version":"vor","delay-in-days":9,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Current Protocols"],"published-print":{"date-parts":[[2024,6]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Sequence changes in viral genomes generate protein sequence diversity that enables viruses to evade the host immune system, hindering the development of effective preventive and therapeutic interventions. The massive proliferation of sequence data provides unprecedented opportunities to study viral adaptation and evolution. An alignment\u2010free approach removes various restrictions posed by an alignment\u2010dependent approach for studying sequence diversity. The publicly available tool, UNIQmin, offers an alignment\u2010free approach for studying viral sequence diversity at any given rank of taxonomy lineage and is big data ready. The tool performs an exhaustive search to determine the minimal set of sequences required to capture the peptidome diversity within a given dataset. This compression is possible through the removal of identical sequences and unique sequences that do not contribute effectively to the peptidome diversity pool. Herein, we describe a detailed four\u2010part protocol utilizing UNIQmin to generate the minimal set for the purpose of viral diversity analyses, alignment\u2010free at any rank of the taxonomy lineage, using the recent global public health threat <jats:italic>Monkeypox virus<\/jats:italic> (MPX) sequence data as a case study. The protocol enables a systematic bioinformatics approach to study sequence diversity across taxonomic lineages, which is crucial for our future preparedness against viral epidemics. This is particularly important when data are abundant, freely available, and alignment is not an option. \u00a9 2024 Wiley Periodicals LLC.<\/jats:p><jats:p><jats:bold>Basic Protocol 1<\/jats:bold>: Tool installation and input file preparation<\/jats:p><jats:p><jats:bold>Basic Protocol 2<\/jats:bold>: Generation of a minimal set of sequences for a given dataset<\/jats:p><jats:p><jats:bold>Basic Protocol 3<\/jats:bold>: Comparative minimal set analysis across taxonomic lineage ranks<\/jats:p><jats:p><jats:bold>Basic Protocol 4<\/jats:bold>: Factors affecting the minimal set of sequences<\/jats:p>","DOI":"10.1002\/cpz1.1056","type":"journal-article","created":{"date-parts":[[2024,6,10]],"date-time":"2024-06-10T15:25:34Z","timestamp":1718033134000},"source":"Crossref","is-referenced-by-count":0,"title":["A Systematic Bioinformatics Approach for Mapping the Minimal Set of a Viral Peptidome"],"prefix":"10.1002","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3574-1365","authenticated-orcid":false,"given":"Li Chuin","family":"Chong","sequence":"first","affiliation":[{"name":"Centre for Bioinformatics, School of Data Sciences Perdana University  Kuala Lumpur Malaysia"},{"name":"Beykoz Institute of Life Sciences and Biotechnology Bezmialem Vakif University  Beykoz Turkey"},{"name":"Current affiliation: Institute for Experimental Virology TWINCORE Centre for Experimental and Clinical Infection Research, a Medical School Hannover (MHH) and Helmholtz Centre for Infection Research (HZI) joint venture  Hannover Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9202-279X","authenticated-orcid":false,"given":"Asif M.","family":"Khan","sequence":"additional","affiliation":[{"name":"Centre for Bioinformatics, School of Data Sciences Perdana University  Kuala Lumpur Malaysia"},{"name":"Beykoz Institute of Life Sciences and Biotechnology Bezmialem Vakif University  Beykoz Turkey"},{"name":"Current affiliation: College of Computing and Information Technology University of Doha for Science and Technology  Doha Qatar"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2024,6,10]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7954"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa1100"},{"key":"e_1_2_8_4_1","first-page":"104","article-title":"Preclinical evaluation of a vaccine based on conserved region of M protein that prevents group A streptococcal infection","volume":"119","author":"Batzloff M.","year":"2004","journal-title":"The Indian Journal of Medical Research"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmpbup.2021.100009"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u201010\u2010421"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/ilar\/ilx026"},{"key":"e_1_2_8_8_1","unstructured":"Centers for Disease Control and Prevention (CDC). (2022).2022 Mpox outbreak global map | Mpox | Poxvirus.https:\/\/www.cdc.gov\/poxvirus\/mpox\/response\/2022\/world\u2010map.html"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baw163"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864\u2010019\u20106311\u2010z"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1101\/2022.10.31.513750"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.3390\/biology10090853"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-12-816331-3.00002-7"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1008271"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41579\u2010021\u201000573\u20100"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw1065"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2021.105106"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0001190"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0059994"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41564\u2010020\u20100709\u2010x"},{"volume-title":"ScholarBank@NUS repository","year":"2005","author":"Khan A. M.","key":"e_1_2_8_21_1"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u20107\u2010S5\u2010S4"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12920\u2010017\u20100301\u20102"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0000272"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.46234\/ccdcw2021.255"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0005352"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl158"},{"issue":"05","key":"e_1_2_8_28_1","first-page":"145","article-title":"MoDa\u2010A data warehouse for multi\u2010\u201cOmics\u201d data","volume":"04","author":"Neogi S. G.","year":"2013","journal-title":"Journal of Data Mining in Genomics & Proteomics"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1189"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1003"},{"key":"e_1_2_8_31_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01031\u201017"},{"key":"e_1_2_8_32_1","first-page":"2.2:1","volume-title":"Phylogenetics in the Genomic era","author":"Ranwez V.","year":"2020"},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev\u2010biodatasci\u2010080917\u2010013431"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa892"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/1.2.190"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.1002\/j.1538\u20107305.1948.tb01338.x"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2016.177"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010018\u201004964\u20105"},{"key":"e_1_2_8_39_1","doi-asserted-by":"publisher","DOI":"10.1002\/9780471650126.dob0322.pub2"},{"volume-title":"ScholarBank@NUS repository","year":"2009","author":"Tan A. H.","key":"e_1_2_8_40_1"},{"key":"e_1_2_8_41_1","doi-asserted-by":"publisher","DOI":"10.3390\/v13050871"},{"key":"e_1_2_8_42_1","unstructured":"Tharanga S. Hu Y. Unlu E. S. Sjaugi M. F. Celik M. A. Hekimoglu H. Miotto O. Oncel M. M. &Khan A. M.(2022).DiMA: Sequence diversity dynamics analyser for viruses.https:\/\/doi.org\/10.48550\/arXiv.2205.13915"},{"key":"e_1_2_8_43_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0018093"},{"key":"e_1_2_8_44_1","doi-asserted-by":"publisher","DOI":"10.1098\/rsif.2009.0560"},{"key":"e_1_2_8_45_1","unstructured":"World Health Organization. (2023).WHO COVID\u201019 dashboard.https:\/\/data.who.int\/dashboards\/covid19\/cases?n=c"},{"key":"e_1_2_8_46_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010017\u20101319\u20107"}],"container-title":["Current Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cpz1.1056","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,11]],"date-time":"2024-12-11T18:23:10Z","timestamp":1733941390000},"score":1,"resource":{"primary":{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/10.1002\/cpz1.1056"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6]]},"references-count":45,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2024,6]]}},"alternative-id":["10.1002\/cpz1.1056"],"URL":"https:\/\/doi.org\/10.1002\/cpz1.1056","archive":["Portico"],"relation":{},"ISSN":["2691-1299","2691-1299"],"issn-type":[{"type":"print","value":"2691-1299"},{"type":"electronic","value":"2691-1299"}],"subject":[],"published":{"date-parts":[[2024,6]]},"article-number":"e1056"}}