{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T03:45:05Z","timestamp":1771386305568,"version":"3.50.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2018,8,7]],"date-time":"2018-08-07T00:00:00Z","timestamp":1533600000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["SFB 1021"],"award-info":[{"award-number":["SFB 1021"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"AquaDiva","award":["INST 275\/367-1"],"award-info":[{"award-number":["INST 275\/367-1"]}]},{"name":"FungiNet","award":["INST 275\/365-1"],"award-info":[{"award-number":["INST 275\/365-1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The protein-coding sequences of messenger RNAs are the linear template for translation of the gene sequence into protein. Nevertheless, the RNA can also form secondary structures by intramolecular base-pairing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We show that the nucleotide distribution within codons is biased in all taxa of life on a global scale. Thereby, RNA secondary structures that require base-pairing between the position 1 of a codon with the position 1 of an opposing codon (here named RNA secondary structure class c1) are under-represented. We conclude that this bias may result from the co-evolution of codon sequence and mRNA secondary structure, suggesting that RNA secondary structures are generally important in protein-coding regions of mRNAs. The above result also implies that codon position 2 has a smaller influence on the amino acid choice than codon position 1.<\/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\/bty678","type":"journal-article","created":{"date-parts":[[2018,8,6]],"date-time":"2018-08-06T19:12:45Z","timestamp":1533582765000},"page":"579-583","source":"Crossref","is-referenced-by-count":20,"title":["Global importance of RNA secondary structures in protein-coding sequences"],"prefix":"10.1093","volume":"35","author":[{"given":"Markus","family":"Fricke","sequence":"first","affiliation":[{"name":"RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany"},{"name":"European Virus Bioinformatics Center (EVBC), Jena, Germany"}]},{"given":"Ruman","family":"Gerst","sequence":"additional","affiliation":[{"name":"European Virus Bioinformatics Center (EVBC), Jena, Germany"}]},{"given":"Bashar","family":"Ibrahim","sequence":"additional","affiliation":[{"name":"RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany"},{"name":"European Virus Bioinformatics Center (EVBC), Jena, Germany"}]},{"given":"Michael","family":"Niepmann","sequence":"additional","affiliation":[{"name":"Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-University, Giessen, Germany"}]},{"given":"Manja","family":"Marz","sequence":"additional","affiliation":[{"name":"RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany"},{"name":"European Virus Bioinformatics Center (EVBC), Jena, Germany"},{"name":"German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany"},{"name":"FLI Leibniz Institute for Age Research, Jena, Germany"}]}],"member":"286","published-online":{"date-parts":[[2018,8,7]]},"reference":[{"key":"2023051510532272700_bty678-B1","doi-asserted-by":"crossref","first-page":"10231","DOI":"10.1073\/pnas.1500012112","article-title":"Why chloroplasts and mitochondria retain their own genomes and genetic systems: colocation for redox regulation of gene expression","volume":"112","author":"Allen","year":"2015","journal-title":"Proc. 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