{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,10]],"date-time":"2025-12-10T09:03:46Z","timestamp":1765357426375,"version":"build-2065373602"},"reference-count":33,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2023,8,11]],"date-time":"2023-08-11T00:00:00Z","timestamp":1691712000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computation"],"abstract":"<jats:p>Background: In present genomes, current relics of a circular RNA appear which could have played a central role as a primitive catalyst of the peptide genesis. Methods: Using a proximity measure to this circular RNA and the distance, a new unsupervised classifier called MaxwellTM has been constructed based on the Burrows\u2013Wheeler transform algorithm. Results: By applying the classifier to numerous genomes from various realms (Bacteria, Archaea, Vegetables and Animals), we obtain phylogenetic trees that are coherent with biological trees based on pure evolutionary arguments. Discussion: We discuss the role of the combinatorial operators responsible for the evolution of the genome of many species. Conclusions: We opened up possibilities for understanding the mechanisms of a primitive factory of peptides represented by an RNA ring. We showed that this ring was able to transmit some of its sub-sequences in the sequences of genes involved in the mechanisms of the current ribosomal production of proteins.<\/jats:p>","DOI":"10.3390\/computation11080158","type":"journal-article","created":{"date-parts":[[2023,8,11]],"date-time":"2023-08-11T10:20:16Z","timestamp":1691749216000},"page":"158","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Genomic Phylogeny Using the MaxwellTM Classifier Based on Burrows\u2013Wheeler Transform"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8335-9240","authenticated-orcid":false,"given":"Jacques","family":"Demongeot","sequence":"first","affiliation":[{"name":"Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France"}]},{"given":"Jo\u00ebl","family":"Gardes","sequence":"additional","affiliation":[{"name":"Orange Labs, 38229 Meylan, France"}]},{"given":"Christophe","family":"Maldivi","sequence":"additional","affiliation":[{"name":"Orange Labs, 38229 Meylan, France"}]},{"given":"Denis","family":"Boisset","sequence":"additional","affiliation":[{"name":"Orange Labs, 38229 Meylan, France"}]},{"given":"Kenza","family":"Boufama","sequence":"additional","affiliation":[{"name":"Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France"}]},{"given":"Im\u00e8ne","family":"Touzouti","sequence":"additional","affiliation":[{"name":"Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France"}]}],"member":"1968","published-online":{"date-parts":[[2023,8,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1126\/science.117.3046.528","article-title":"A Production of amino acids under possible primitive Earth conditions","volume":"117","author":"Miller","year":"1953","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1126\/science.1085145","article-title":"Prebiotic soup\u2014Revisiting the Miller experiment","volume":"300","author":"Bada","year":"2003","journal-title":"Science"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1089\/ast.2019.2045","article-title":"The Hot Spring Hypothesis for an Origin of Life","volume":"20","author":"Damer","year":"2020","journal-title":"Astrobiology"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1007\/BF00625709","article-title":"Prebiotic synthesis of biopolymers on inorganic templates","volume":"60","author":"Katchalsky","year":"1973","journal-title":"Naturwiss"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1887","DOI":"10.1098\/rstb.2006.1881","article-title":"On the origin of biochemistry at an alkaline hydrothermal vent","volume":"362","author":"Martin","year":"2007","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Deamer, D. (2017). The Role of Lipid Membranes in Life\u2019s Origin. Life, 7.","DOI":"10.3390\/life7010005"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1007\/s00239-012-9501-8","article-title":"The Plausibility of RNA-Templated Peptides: Simultaneous RNA Affinity for Adjacent Peptide Side Chains","volume":"74","author":"Puthenvedu","year":"2012","journal-title":"J. Mol. Evol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1038\/nature07033","article-title":"Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme","volume":"454","author":"Xiao","year":"2008","journal-title":"Nature"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1038\/s41589-022-00982-z","article-title":"Structure and mechanism of a methyltransferase ribozyme","volume":"18","author":"Deng","year":"2022","journal-title":"Nat. Chem. Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1107\/S0907444902019066","article-title":"Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme","volume":"59","author":"Milovanovic","year":"2003","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"ref_11","unstructured":"Demongeot, J. (1975). Au Sujet de Quelques Mod\u00e8les Stochastiques Appliqu\u00e9s \u00e0 la Biologie. Mod\u00e9lisation et Simulation, Universit\u00e9 Joseph-Fourier."},{"key":"ref_12","first-page":"61","article-title":"Sur la possibilit\u00e9 de consid\u00e9rer le code g\u00e9n\u00e9tique comme un code \u00e0 encha\u00eenement","volume":"62","author":"Demongeot","year":"1978","journal-title":"Rev. Biomaths"},{"key":"ref_13","first-page":"807","article-title":"Code g\u00e9n\u00e9tique et codes \u00e0 encha\u00eenement","volume":"296","author":"Demongeot","year":"1983","journal-title":"C. R. Seances L\u2019Acad. Sci. Ser. III"},{"key":"ref_14","unstructured":"(2023, May 23). GtRNAdB. Available online: http:\/\/gtrnadb.ucsc.edu\/."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.jtbi.2007.07.010","article-title":"A circular RNA at the origin of life","volume":"249","author":"Demongeot","year":"2007","journal-title":"J. Theor. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/S0273-1177(99)80108-2","article-title":"Direct interaction between amino-acids and nucleotides as a possible physico-chemical basis for the origin of the genetic code","volume":"15","author":"Hobish","year":"1995","journal-title":"Adv. Space Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1073\/pnas.98.4.1393","article-title":"Oligonucleotide-directed peptide synthesis in a ribosome- and ribozyme-free system","volume":"98","author":"Tamura","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1038\/228636a0","article-title":"Prebiotic synthesis of polypeptides by heterogeneous polycondensation of amino-acid adenylates","volume":"228","author":"Berger","year":"1970","journal-title":"Nature"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1007\/BF00623322","article-title":"Selforganization of matter and the evolution of biological macromolecules","volume":"58","author":"Eigen","year":"1971","journal-title":"Naturwissenschaften"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/319618a0","article-title":"Origin of life: The RNA world","volume":"319","author":"Gilbert","year":"1986","journal-title":"Nature"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"34","DOI":"10.3390\/life1010034","article-title":"Approaches to the origin of life on Earth","volume":"1","author":"Kauffman","year":"2011","journal-title":"Life"},{"key":"ref_22","unstructured":"(2023, May 23). NCBI, Available online: https:\/\/www.ncbi.nlm.nih.gov\/refseq\/."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"47","DOI":"10.13189\/ms.2018.060401","article-title":"A Simple Approximation for Normal Distribution Function","volume":"6","author":"Edous","year":"2018","journal-title":"Math. Stat."},{"key":"ref_24","first-page":"1464","article-title":"Maxwell\u00ae: An unsupervised learning approach for 5P medicine","volume":"264","author":"Gardes","year":"2019","journal-title":"Stud. Health Technol. Inform."},{"key":"ref_25","first-page":"10009821328","article-title":"A block-sorting lossless data compression algorithm","volume":"124","author":"Burrows","year":"1994","journal-title":"Digit. SRC Res. Rep."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1109\/TIT.2005.844059","article-title":"Clustering by compression","volume":"51","author":"Cilibrasi","year":"2005","journal-title":"IEEE Trans. Inf. Theory"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1602","DOI":"10.1109\/TPAMI.2014.2375175","article-title":"Normalized Compression Distance of Multisets with Applications","volume":"37","author":"Cohen","year":"2015","journal-title":"IEEE Trans. PAMI"},{"key":"ref_28","unstructured":"(2023, May 23). Graphviz. Available online: https:\/\/graphviz.org\/."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/BF01796132","article-title":"The concept of cellular evolution","volume":"10","author":"Woese","year":"1977","journal-title":"J. Mol. Evol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"16229","DOI":"10.1038\/nmicrobiol.2016.229","article-title":"Is LUCA a thermophilic progenote?","volume":"1","author":"Gogarten","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2407","DOI":"10.1038\/ismej.2017.122","article-title":"The growing tree of Archaea: New perspectives on their diversity, evolution and ecology","volume":"11","author":"Adam","year":"2017","journal-title":"ISME J."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0304-3975(00)00406-0","article-title":"Theory of Genetic Algorithms","volume":"259","author":"Schmitt","year":"2001","journal-title":"Theor. Comput. Sci."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Ighalo, J.O., and Marques, G. (2022). Current Trends and Advances in Computer-Aided Intelligent Environmental Data Engineering, Elsevier.","DOI":"10.1016\/B978-0-323-85597-6.00012-4"}],"container-title":["Computation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-3197\/11\/8\/158\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T20:31:42Z","timestamp":1760128302000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-3197\/11\/8\/158"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,11]]},"references-count":33,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2023,8]]}},"alternative-id":["computation11080158"],"URL":"https:\/\/doi.org\/10.3390\/computation11080158","relation":{},"ISSN":["2079-3197"],"issn-type":[{"type":"electronic","value":"2079-3197"}],"subject":[],"published":{"date-parts":[[2023,8,11]]}}}