{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T02:10:34Z","timestamp":1780539034669,"version":"3.54.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,13]],"date-time":"2022-12-13T00:00:00Z","timestamp":1670889600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["F31-HG010984"],"award-info":[{"award-number":["F31-HG010984"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01-HG009116"],"award-info":[{"award-number":["R01-HG009116"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]}],"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>Summary<\/jats:title>\n                  <jats:p>Codetta is a Python program for predicting the genetic code table of an organism from nucleotide sequences. Codetta can analyze an arbitrary nucleotide sequence and needs no sequence annotation or taxonomic placement. The most likely amino acid decoding for each of the 64 codons is inferred from alignments of profile hidden Markov models of conserved proteins to the input sequence.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Codetta 2.0 is implemented as a Python 3 program for MacOS and Linux and is available from http:\/\/eddylab.org\/software\/codetta\/codetta2.tar.gz and at http:\/\/github.com\/kshulgina\/codetta.<\/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\/btac802","type":"journal-article","created":{"date-parts":[[2022,12,12]],"date-time":"2022-12-12T16:35:51Z","timestamp":1670862951000},"source":"Crossref","is-referenced-by-count":29,"title":["Codetta: predicting the genetic code from nucleotide sequence"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7658-9294","authenticated-orcid":false,"given":"Yekaterina","family":"Shulgina","sequence":"first","affiliation":[{"name":"Department of Molecular and Cellular Biology, Harvard University , Cambridge, MA 02138, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6676-4706","authenticated-orcid":false,"given":"Sean R","family":"Eddy","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology, Harvard University , Cambridge, MA 02138, USA"},{"name":"Howard Hughes Medical Institute, Harvard University , Cambridge, MA 02138, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,13]]},"reference":[{"key":"2023010805413334800_btac802-B1","doi-asserted-by":"crossref","first-page":"W389","DOI":"10.1093\/nar\/gkl044","article-title":"GenDecoder: genetic code prediction for metazoan mitochondria","volume":"34","author":"Abascal","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023010805413334800_btac802-B2","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/s41564-022-01128-6","article-title":"Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes","volume":"7","author":"Borges","year":"2022","journal-title":"Nat. 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