{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:11:06Z","timestamp":1772165466368,"version":"3.50.1"},"reference-count":53,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,4,4]],"date-time":"2023-04-04T00:00:00Z","timestamp":1680566400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,4,4]],"date-time":"2023-04-04T00:00:00Z","timestamp":1680566400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Concentrations of the pathogenic microorganisms\u2019 DNA in biological samples are typically low. Therefore, DNA diagnostics of common infections are costly, rarely accurate, and challenging. Limited by failing to cover updated epidemic testing samples, computational services are difficult to implement in clinical applications without complex customized settings. Furthermore, the combined biomarkers used to maintain high conservation may not be cost effective and could cause several experimental errors in many clinical settings. Given the limitations of recent developed technology, 16S rRNA is too conserved to distinguish closely related species, and mosaic plasmids are not effective as well because of their uneven distribution across prokaryotic taxa.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Here, we provide a computational strategy, Shine, that allows extraction of specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets. Distinguished with simple concatenations with blast-based filtering, our method involves a de novo genome alignment-based pipeline to explore the original and specific repetitive biomarkers in the defined population. It can cover all members to detect newly discovered multicopy conserved species-specific or even subspecies-specific target probes and primer sets. The method has been successfully applied to a number of clinical projects and has the overwhelming advantages of automated detection of all pathogenic microorganisms without the limitations of genome annotation and incompletely assembled motifs. Using on our pipeline, users may select different configuration parameters depending on the purpose of the project for routine clinical detection practices on the website\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/bioinfo.liferiver.com.cn\">https:\/\/bioinfo.liferiver.com.cn<\/jats:ext-link>\n                      with easy registration.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The proposed strategy is suitable for identifying shared phylogenetic markers while featuring low rates of false positive or false negative. This technology is suitable for the automatic design of minimal and efficient PCR primers and other types of detection probes.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-023-05195-2","type":"journal-article","created":{"date-parts":[[2023,4,4]],"date-time":"2023-04-04T07:07:39Z","timestamp":1680592059000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Shine: A novel strategy to extract specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets"],"prefix":"10.1186","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7012-0193","authenticated-orcid":false,"given":"Cong","family":"Ji","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junbin","family":"Shao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2023,4,4]]},"reference":[{"issue":"3","key":"5195_CR1","doi-asserted-by":"publisher","first-page":"327","DOI":"10.4103\/0971-5916.198677","volume":"144","author":"B Priyanka","year":"2016","unstructured":"Priyanka B, Patil R, Dwarakanath S. A review on detection methods used for foodborne pathogens. Indian J Med Res. 2016;144(3):327\u201338.","journal-title":"Indian J Med Res"},{"issue":"2","key":"5195_CR2","doi-asserted-by":"publisher","first-page":"122","DOI":"10.3390\/pathogens9020122","volume":"9","author":"A Upadhyay","year":"2020","unstructured":"Upadhyay A, Yang H, Zaman B, Zhang L, Wu Y, Wang J, et al. ZnO nanoflower-based NanoPCR as an efficient diagnostic tool for quick diagnosis of canine vector-borne pathogens. Pathogens. 2020;9(2):122.","journal-title":"Pathogens"},{"issue":"2","key":"5195_CR3","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/S0167-8809(97)00030-3","volume":"64","author":"RTV Fox","year":"1997","unstructured":"Fox RTV. The present and future use of technology to detect plant pathogens to guide disease control in sustainable farming systems. Agr Ecosyst Environ. 1997;64(2):125\u201332.","journal-title":"Agr Ecosyst Environ"},{"key":"5195_CR4","doi-asserted-by":"crossref","unstructured":"Anahtar MN, Shaw BM, Slater D, Byrne EH, Botti-Lodovico Y, Adams G, et al. Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay. Journal of Clinical Pathology, 2021: p. jclinpath-2020-207128.","DOI":"10.1101\/2020.08.26.20157297"},{"issue":"2","key":"5195_CR5","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1039\/C8AN01488D","volume":"144","author":"P Rajapaksha","year":"2019","unstructured":"Rajapaksha P, Elbourne A, Gangadoo S, Brown R, Cozzolino D, Chapman J. A review of methods for the detection of pathogenic microorganisms. Analyst. 2019;144(2):396\u2013411.","journal-title":"Analyst"},{"key":"5195_CR6","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1007\/978-1-4939-2365-6_13","volume":"1275","author":"B Thornton","year":"2015","unstructured":"Thornton B, Basu C. Rapid and simple method of qPCR primer design. Methods Mol Biol. 2015;1275:173\u20139.","journal-title":"Methods Mol Biol"},{"issue":"1","key":"5195_CR7","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1111\/j.1574-6941.2008.00629.x","volume":"67","author":"CJ Smith","year":"2009","unstructured":"Smith CJ, Osborn AM. Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiol Ecol. 2009;67(1):6\u201320.","journal-title":"FEMS Microbiol Ecol"},{"issue":"1","key":"5195_CR8","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.jviromet.2004.11.016","volume":"125","author":"EA Lusi","year":"2005","unstructured":"Lusi EA, Guarascio P, Presutti C, Villani R, Pellicelli A, Soccorsi F. One-step nested PCR for detection of 2 LTR circles in PBMCs of HIV-1 infected patients with no detectable plasma HIV RNA. J Virol Methods. 2005;125(1):11\u20133.","journal-title":"J Virol Methods"},{"issue":"1","key":"5195_CR9","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/s13052-020-0770-3","volume":"46","author":"J Thomas","year":"2020","unstructured":"Thomas J, Pociute A, Kevalas R, Malinauskas M, Jankauskaite\u00a0L. Blood biomarkers differentiating viral versus bacterial pneumonia aetiology: a literature review. Ital J Pediatr. 2020;46(1):4\u20134.","journal-title":"Ital J Pediatr"},{"issue":"11","key":"5195_CR10","doi-asserted-by":"publisher","first-page":"1349","DOI":"10.1093\/bioinformatics\/btp241","volume":"25","author":"T Koressaar","year":"2009","unstructured":"Koressaar T, Joers K, Remm M. Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms. Bioinformatics. 2009;25(11):1349\u201355.","journal-title":"Bioinformatics"},{"key":"5195_CR11","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1016\/j.envint.2018.11.054","volume":"123","author":"TM Fumian","year":"2019","unstructured":"Fumian TM, Fioretti JM, Lun JH, dos Santos IAL, White PA, Miagostovich MP. Detection of norovirus epidemic genotypes in raw sewage using next generation sequencing. Environ Int. 2019;123:282\u201391.","journal-title":"Environ Int"},{"issue":"4","key":"5195_CR12","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1164\/rccm.201506-1100OC","volume":"193","author":"C Valim","year":"2016","unstructured":"Valim C, Ahmad R, Lanaspa M, Tan Y, Ac\u00e1cio S, Gillette MA, et al. Responses to bacteria, virus, and malaria distinguish the etiology of pediatric clinical pneumonia. Am J Respir Crit Care Med. 2016;193(4):448\u201359.","journal-title":"Am J Respir Crit Care Med"},{"issue":"4","key":"5195_CR13","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1016\/j.diagmicrobio.2014.04.006","volume":"79","author":"MA Elemraid","year":"2014","unstructured":"Elemraid MA,\u00a0Rushton SP, Thomas MF, Spencer DA, Gennery AR, Clark JE. Utility of inflammatory markers in predicting the aetiology of pneumonia in children. Diagn Microbiol Infect Dis. 2014;79(4):458\u201362.","journal-title":"Diagn Microbiol Infect Dis"},{"key":"5195_CR14","doi-asserted-by":"crossref","unstructured":"Naydenova E, Tsanas A, Howie S, Casals-Pascual C, De Vos M. The power of data mining in diagnosis of childhood pneumonia. J R Soc Interface, 2016. 13(120).","DOI":"10.1098\/rsif.2016.0266"},{"key":"5195_CR15","unstructured":"van Hattem JM, de Wever B. 16S rRNA sequence analysis: application and pitfalls. Ned Tijdschr Geneeskd, 2019;163."},{"issue":"6","key":"5195_CR16","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1101\/gr.241299.118","volume":"29","author":"D Antipov","year":"2019","unstructured":"Antipov D,\u00a0Raiko M, Lapidus A, Pevzner PA. Plasmid detection and assembly in genomic and metagenomic data sets. Genome Res. 2019;29(6):961\u20138.","journal-title":"Genome Res"},{"issue":"4","key":"5195_CR17","doi-asserted-by":"publisher","first-page":"840","DOI":"10.1128\/CMR.17.4.840-862.2004","volume":"17","author":"JE Clarridge 3rd","year":"2004","unstructured":"Clarridge JE. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev. 2004;17(4):840\u201362.","journal-title":"Clin Microbiol Rev"},{"issue":"2","key":"5195_CR18","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1016\/j.mimet.2007.02.005","volume":"69","author":"S Chakravorty","year":"2007","unstructured":"Chakravorty S, Helb D, Burday M, Connell N, Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods. 2007;69(2):330\u20139.","journal-title":"J Microbiol Methods"},{"issue":"11","key":"5195_CR19","doi-asserted-by":"publisher","first-page":"5445","DOI":"10.1128\/AEM.68.11.5445-5451.2002","volume":"68","author":"T Matsuki","year":"2002","unstructured":"Matsuki T, Watanabe K, Fujimoto J, Miyamoto Y, Takada T, Matsumoto K, et al. Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl Environ Microbiol. 2002;68(11):5445\u201351.","journal-title":"Appl Environ Microbiol"},{"issue":"4","key":"5195_CR20","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1007\/BF03262067","volume":"6","author":"JB Patel","year":"2001","unstructured":"Patel JB. 16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory. Mol Diagn. 2001;6(4):313\u201321.","journal-title":"Mol Diagn"},{"issue":"1","key":"5195_CR21","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1186\/s12864-019-5641-1","volume":"20","author":"JL Sevigny","year":"2019","unstructured":"Sevigny JL, Rothenheber D, Diaz KS, Zhang Y, Agustsson K, Bergeron RD, et al. Marker genes as predictors of shared genomic function. BMC Genomics. 2019;20(1):268.","journal-title":"BMC Genomics"},{"key":"5195_CR22","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/j.plasmid.2019.02.003","volume":"102","author":"MW Pesesky","year":"2019","unstructured":"Pesesky MW, Tilley R, Beck DAC. Mosaic plasmids are abundant and unevenly distributed across prokaryotic taxa. Plasmid. 2019;102:10\u20138.","journal-title":"Plasmid"},{"issue":"10","key":"5195_CR23","doi-asserted-by":"publisher","first-page":"2731","DOI":"10.1093\/molbev\/msr121","volume":"28","author":"K Tamura","year":"2011","unstructured":"Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28(10):2731\u20139.","journal-title":"Mol Biol Evol"},{"issue":"8","key":"5195_CR24","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","volume":"24","author":"Z Yang","year":"2007","unstructured":"Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586\u201391.","journal-title":"Mol Biol Evol"},{"issue":"9","key":"5195_CR25","doi-asserted-by":"publisher","first-page":"3408","DOI":"10.1128\/JB.00009-08","volume":"190","author":"A Coros","year":"2008","unstructured":"Coros A, DeConno E, Derbyshire KM. IS6110, a Mycobacterium tuberculosis complex-specific insertion sequence, is also present in the genome of Mycobacterium smegmatis, suggestive of lateral gene transfer among mycobacterial species. J Bacteriol. 2008;190(9):3408\u201310.","journal-title":"J Bacteriol"},{"issue":"11","key":"5195_CR26","doi-asserted-by":"publisher","first-page":"3631","DOI":"10.1128\/JCM.00970-13","volume":"51","author":"MI Millan-Lou","year":"2013","unstructured":"Millan-Lou MI, L\u00f3pez-Calleja AI, Colmenarejo C, Lezcano MA, Vitoria MA, del Portillo P, et al. Global study of IS6110 in a successful Mycobacterium tuberculosis strain: clues for deciphering its behavior and for its rapid detection. J Clin Microbiol. 2013;51(11):3631\u20137.","journal-title":"J Clin Microbiol"},{"issue":"3","key":"5195_CR27","doi-asserted-by":"publisher","first-page":"640","DOI":"10.1099\/00207713-46-3-640","volume":"46","author":"D Van","year":"1996","unstructured":"Zee AVD, Groenendijk H, Peeters M, Mooi FR. The differentiation of Bordetella parapertussis and Bordetella bronchiseptica\u00a0from humans and animals as determined by DNA polymorphism mediated by two different insertion sequence elements suggests their phylogenetic relationship. Int J Syst Bacteriol. 1996;46(3):640\u20137.","journal-title":"Int J Syst Bacteriol"},{"issue":"13","key":"5195_CR28","doi-asserted-by":"publisher","first-page":"30494","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","volume":"22","author":"Y Shu","year":"2017","unstructured":"Shu Y, McCauley J. GISAID: Global initiative on sharing all influenza data-from vision to reality. Euro Surveill. 2017;22(13):30494.","journal-title":"Euro Surveill"},{"key":"5195_CR29","doi-asserted-by":"publisher","first-page":"e05378","DOI":"10.7554\/eLife.05378","volume":"4","author":"C-X Li","year":"2015","unstructured":"Li CX, Shi M, Tian JH, Lin XD, Kang YJ, Chen LJ, et al. Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. eLife. 2015;4:e05378.","journal-title":"eLife"},{"key":"5195_CR30","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.coviro.2018.07.017","volume":"31","author":"YZ Zhang","year":"2018","unstructured":"Zhang YZ, Wu WC, Shi M, Holmes EC. The diversity, evolution and origins of vertebrate RNA viruses. Curr Opin Virol. 2018;31:9\u201316.","journal-title":"Curr Opin Virol"},{"issue":"10","key":"5195_CR31","doi-asserted-by":"publisher","first-page":"e26047","DOI":"10.1371\/journal.pone.0026047","volume":"6","author":"MA Poritz","year":"2011","unstructured":"Poritz MA, Blaschke AJ, Byington CL, Meyers L, Nilsson K, Jones DE,et al. FilmArray, an automated nested multiplex PCR system for multi-pathogen detection: development and application to respiratory tract infection. PLoS ONE. 2011;6(10):e26047.","journal-title":"PLoS ONE"},{"key":"5195_CR32","doi-asserted-by":"crossref","unstructured":"Koo SH, Jiang B, Lim PQ, La MV, Tan TY. Development of a rapid multiplex PCR assay for the detection of common pathogens associated with community-acquired pneumonia. Transactions of The Royal Society of Tropical Medicine and Hygiene, 2021.","DOI":"10.1093\/trstmh\/trab079"},{"key":"5195_CR33","doi-asserted-by":"publisher","unstructured":"Moutaouakil AEl, Poovathy S, Belmoubarik M, Peng WK. Review: Graphene-based biosensor for Viral Detection. 2020. https:\/\/doi.org\/10.48550\/arXiv.2006.11881.","DOI":"10.48550\/arXiv.2006.11881"},{"key":"5195_CR34","doi-asserted-by":"publisher","first-page":"112436","DOI":"10.1016\/j.bios.2020.112436","volume":"166","author":"E Vermisoglou","year":"2020","unstructured":"Vermisoglou E, Pan\u00e1\u010dek D, Jayaramulu K, Pykal M, Fr\u00e9bort I, Kol\u00e1\u0159 M, et al. Human virus detection with graphene-based materials. Biosens Bioelectron. 2020;166:112436.","journal-title":"Biosens Bioelectron"},{"issue":"1","key":"5195_CR35","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/s12951-018-0400-z","volume":"16","author":"J Pena-Bahamonde","year":"2018","unstructured":"Pena-Bahamonde J, Nguyen HN, Fanourakis SK, Rodrigues DF. Recent advances in graphene-based biosensor technology with applications in life sciences. J Nanobiotechnol. 2018;16(1):75.","journal-title":"J Nanobiotechnol"},{"key":"5195_CR36","doi-asserted-by":"publisher","DOI":"10.1101\/2020.09.02.279737","author":"I Das Jana","year":"2020","unstructured":"Das JI, Kumbhakar P, Banerjee S, Gowda CC, Kedia N, Kuila SK, et al. Development of a copper-graphene nanocomposite based transparent coating with antiviral activity against influenza virus. BioRxiv. 2020. https:\/\/doi.org\/10.1101\/2020.09.02.279737.","journal-title":"BioRxiv"},{"issue":"5","key":"5195_CR37","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1016\/j.chom.2021.04.003","volume":"29","author":"CA Freije","year":"2021","unstructured":"Freije CA, Sabeti PC. Detect and destroy: CRISPR-based technologies for the response against viruses. Cell Host Microbe. 2021;29(5):689\u2013703.","journal-title":"Cell Host Microbe"},{"issue":"15","key":"5195_CR38","doi-asserted-by":"publisher","first-page":"1492","DOI":"10.1056\/NEJMc2026172","volume":"383","author":"J Joung","year":"2020","unstructured":"Joung J, Ladha A, Saito M, Kim NG, Woolley AE, Segel M, et al. Detection of SARS-CoV-2 with SHERLOCK one-pot testing. N Engl J Med. 2020;383(15):1492\u20134.","journal-title":"N Engl J Med"},{"issue":"3","key":"5195_CR39","doi-asserted-by":"publisher","first-page":"e1009318","DOI":"10.1371\/journal.ppat.1009318","volume":"17","author":"AE Gorbalenya","year":"2021","unstructured":"Gorbalenya AE, Siddell SG. Recognizing species as a new focus of virus research. PLoS Pathog. 2021;17(3):e1009318\u2013e1009318.","journal-title":"PLoS Pathog"},{"issue":"D1","key":"5195_CR40","doi-asserted-by":"publisher","first-page":"D73","DOI":"10.1093\/nar\/gkv1226","volume":"44","author":"PA Kitts","year":"2016","unstructured":"Kitts PA, Church DM, Thibaud-Nissen F, Choi J, Hem V, Sapojnikov V, et al. Assembly: a resource for assembled genomes at NCBI. Nucleic Acids Res. 2016;44(D1):D73-80.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"5195_CR41","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1002\/gch2.1018","volume":"1","author":"S Elbe","year":"2017","unstructured":"Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID\u2019s innovative contribution to global health. Glob Chall. 2017;1(1):33\u201346.","journal-title":"Glob Chall"},{"issue":"5","key":"5195_CR42","doi-asserted-by":"publisher","first-page":"1613","DOI":"10.1099\/ijsem.0.001755","volume":"67","author":"SH Yoon","year":"2017","unstructured":"Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2017;67(5):1613\u20137.","journal-title":"Int J Syst Evol Microbiol"},{"key":"5195_CR43","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1007\/978-1-4939-7737-6_5","volume-title":"Eukaryotic genomic databases: methods and protocols","author":"S Warrenfeltz","year":"2018","unstructured":"Warrenfeltz S, Basenko EY, Crouch K, Harb OS, Kissinger JC, Roos DS, et al. EuPathDB: the eukaryotic pathogen genomics database resource.\u00a0Methods Mol Biol. 2018;1757:69-113."},{"issue":"suppl_1","key":"5195_CR44","doi-asserted-by":"publisher","first-page":"D526","DOI":"10.1093\/nar\/gkn631","volume":"37","author":"C Aurrecoechea","year":"2009","unstructured":"Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, Fischer S, et al. GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res. 2009;37(suppl_1):D526\u201330.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"5195_CR45","doi-asserted-by":"publisher","first-page":"39","DOI":"10.3390\/jof4010039","volume":"4","author":"EY Basenko","year":"2018","unstructured":"Basenko EY, Pulman JA, Shanmugasundram A, Harb OS, Crouch K, Starns D, et al. FungiDB: an integrated bioinformatic resource for fungi and oomycetes. J Fungi. 2018;4(1):39.","journal-title":"J Fungi"},{"issue":"D1","key":"5195_CR46","first-page":"D606","volume":"48","author":"JJ Davis","year":"2020","unstructured":"Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R, Butler RM, et al. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 2020;48(D1):D606\u201312.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"5195_CR47","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"FA Stephen","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search toolBasic local alignment search tool. J Mol Biol. 1990;215(3):403\u201310.","journal-title":"J Mol Biol"},{"issue":"3","key":"5195_CR48","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"SB Needleman","year":"1970","unstructured":"Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970;48(3):443\u201353.","journal-title":"J Mol Biol"},{"key":"5195_CR49","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith TF, MS W. Identification of common molecular subsequences. J Mol Biol. 1981;147:195\u20137.","journal-title":"J Mol Biol"},{"issue":"4","key":"5195_CR50","first-page":"656","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ. BLAT\u2013the BLAST-like alignment tool. Genome Res. 2002;12(4):656\u201364.","journal-title":"Genome Res"},{"issue":"19","key":"5195_CR51","doi-asserted-by":"publisher","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","volume":"26","author":"RC Edgar","year":"2010","unstructured":"Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26(19):2460\u20131.","journal-title":"Bioinformatics"},{"issue":"4","key":"5195_CR52","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772\u201380.","journal-title":"Mol Biol Evol"},{"key":"5195_CR53","doi-asserted-by":"crossref","unstructured":"Untergasser A, Cutcutache L, Koressaar T, Ye J, Faircloth BC, Remm M. Primer3\u2013new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115\u2013e115.","DOI":"10.1093\/nar\/gks596"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05195-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-023-05195-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05195-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,4]],"date-time":"2023-04-04T08:05:11Z","timestamp":1680595511000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-023-05195-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,4]]},"references-count":53,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["5195"],"URL":"https:\/\/doi.org\/10.1186\/s12859-023-05195-2","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-1481582\/v1","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,4,4]]},"assertion":[{"value":"23 March 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 February 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 April 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All protocols were approved by the Liferiver Science and Technology Institute, Shanghai ZJ Bio-Tech Co., Ltd and Use Committee (Shanghai, China).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent to publish"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"128"}}