{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T22:46:44Z","timestamp":1780958804588,"version":"3.54.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T00:00:00Z","timestamp":1669593600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Centre National de la Recherche Scientifque"},{"DOI":"10.13039\/501100019973","name":"Minist\u00e8re de l\u2019Enseignement Sup\u00e9rieur et de la Recherche","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100019973","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Union and FEDER"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Comparing single-stranded nucleic acids (ssNAs) secondary structures is fundamental when investigating their function and evolution and predicting the effect of mutations on their structures. Many comparison metrics exist, although they are either too elaborate or not sensitive enough to distinguish close ssNAs structures.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this context, we developed AptaMat, a simple and sensitive algorithm for ssNAs secondary structures comparison based on matrices representing the ssNAs secondary structures and a metric built upon the Manhattan distance in the plane. We applied AptaMat to several examples and compared the results to those obtained by the most frequently used metrics, namely the Hamming distance and the RNAdistance, and by a recently developed image-based approach. We showed that AptaMat is able to discriminate between similar sequences, outperforming all the other here considered metrics. In addition, we showed that AptaMat was able to correctly classify 14 RFAM families within a clustering procedure.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The python code for AptaMat is available at https:\/\/github.com\/GEC-git\/AptaMat.git.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac752","type":"journal-article","created":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T08:31:07Z","timestamp":1669624267000},"source":"Crossref","is-referenced-by-count":4,"title":["AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures"],"prefix":"10.1093","volume":"39","author":[{"given":"Thomas","family":"Binet","sequence":"first","affiliation":[{"name":"Universit\u00e9 de technologie de Compi\u00e8gne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu, CS 60 319 - 60 203, Compi\u00e8gne Cedex , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B\u00e9rang\u00e8re","family":"Avalle","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de technologie de Compi\u00e8gne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu, CS 60 319 - 60 203, Compi\u00e8gne Cedex , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miraine","family":"D\u00e1vila Felipe","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de technologie de Compi\u00e8gne, LMAC (Laboratory of Applied Mathematics of Compi\u00e8gne), CS 60 319 - 60 203, Compi\u00e8gne Cedex , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4524-1137","authenticated-orcid":false,"given":"Irene","family":"Maffucci","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de technologie de Compi\u00e8gne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu, CS 60 319 - 60 203, Compi\u00e8gne Cedex , France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,11,28]]},"reference":[{"key":"2023010107524267800_btac752-B1","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1261\/rna.903510","article-title":"Comparing RNA secondary structures using a relaxed base-pair score","volume":"16","author":"Agius","year":"2010","journal-title":"RNA"},{"key":"2023010107524267800_btac752-B2","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1093\/bib\/bbq059","article-title":"Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction","volume":"12","author":"Barash","year":"2011","journal-title":"Brief. 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