Classifying Coding DNA with Nucleotide Statistics

Detalhes bibliográficos
Autor(a) principal: Carels, Nicolas
Data de Publicação: 2009
Outros Autores: Frías, Diego
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/31046
Resumo: Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil.
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spelling Carels, NicolasFrías, Diego2019-01-15T14:59:15Z2019-01-15T14:59:15Z2009CARELS, Nicolas; FRÍAS, Diego. Classifying Coding DNA with Nucleotide Statistics. Bioinformatics and Biology Insights, v. 3, p. 141–154, 2009.1177-9322https://www.arca.fiocruz.br/handle/icict/31046engLibertas AcademicaGenômicaCorrelação universalRecursos de codificaçãoViés purinasQuadro de leitura abertaCodon ancestralGenomicsUniversal correlationPurines biasCoding featuresOpen reading frameAncestral codonClassifying Coding DNA with Nucleotide Statisticsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil.Universidade do Estado da Bahia. Departamento de Ciências Exatas e da Terra. Salvador, BA, Brasil.In this report, we compared the success rate of classification of coding sequences (CDS) vs. introns by Codon Structure Factor (CSF) and by a method that we called Universal Feature Method (UFM). UFM is based on the scoring of purine bias (Rrr) and stop codon frequency. We show that the success rate of CDS/intron classification by UFM is higher than by CSF. UFM classifies ORFs as coding or non-coding through a score based on (i) the stop codon distribution, (ii) the product of purine probabilities in the three positions of nucleotide triplets, (iii) the product of Cytosine (C), Guanine (G), and Adenine (A) probabilities in the 1st, 2nd, and 3rd positions of triplets, respectively, (iv) the probabilities of G in 1st and 2nd position of triplets and (v) the distance of their GC3 vs. GC2 levels to the regression line of the universal correlation. More than 80% of CDSs (true positives) of Homo sapiens (250 bp), Drosophila melanogaster (250 bp) and Arabidopsis thaliana (200 bp) are successfully classified with a false positive rate lower or equal to 5%. The method releases coding sequences in their coding strand and coding frame, which allows their automatic translation into protein sequences with 95% confidence. The method is a natural consequence of the compositional bias of nucleotides in coding sequences.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/31046/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALnicolascarels_diegofrias_IOC_2009.pdfnicolascarels_diegofrias_IOC_2009.pdfapplication/pdf1845444https://www.arca.fiocruz.br/bitstream/icict/31046/2/nicolascarels_diegofrias_IOC_2009.pdf35976ccb1b903a644a71f3558e883d97MD52TEXTnicolascarels_diegofrias_IOC_2009.pdf.txtnicolascarels_diegofrias_IOC_2009.pdf.txtExtracted texttext/plain52890https://www.arca.fiocruz.br/bitstream/icict/31046/3/nicolascarels_diegofrias_IOC_2009.pdf.txt83f22f719d541065bef1c99621949db4MD53icict/310462023-09-05 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dc.title.pt_BR.fl_str_mv Classifying Coding DNA with Nucleotide Statistics
title Classifying Coding DNA with Nucleotide Statistics
spellingShingle Classifying Coding DNA with Nucleotide Statistics
Carels, Nicolas
Genômica
Correlação universal
Recursos de codificação
Viés purinas
Quadro de leitura aberta
Codon ancestral
Genomics
Universal correlation
Purines bias
Coding features
Open reading frame
Ancestral codon
title_short Classifying Coding DNA with Nucleotide Statistics
title_full Classifying Coding DNA with Nucleotide Statistics
title_fullStr Classifying Coding DNA with Nucleotide Statistics
title_full_unstemmed Classifying Coding DNA with Nucleotide Statistics
title_sort Classifying Coding DNA with Nucleotide Statistics
author Carels, Nicolas
author_facet Carels, Nicolas
Frías, Diego
author_role author
author2 Frías, Diego
author2_role author
dc.contributor.author.fl_str_mv Carels, Nicolas
Frías, Diego
dc.subject.other.pt_BR.fl_str_mv Genômica
Correlação universal
Recursos de codificação
Viés purinas
Quadro de leitura aberta
Codon ancestral
topic Genômica
Correlação universal
Recursos de codificação
Viés purinas
Quadro de leitura aberta
Codon ancestral
Genomics
Universal correlation
Purines bias
Coding features
Open reading frame
Ancestral codon
dc.subject.en.pt_BR.fl_str_mv Genomics
Universal correlation
Purines bias
Coding features
Open reading frame
Ancestral codon
description Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil.
publishDate 2009
dc.date.issued.fl_str_mv 2009
dc.date.accessioned.fl_str_mv 2019-01-15T14:59:15Z
dc.date.available.fl_str_mv 2019-01-15T14:59:15Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv CARELS, Nicolas; FRÍAS, Diego. Classifying Coding DNA with Nucleotide Statistics. Bioinformatics and Biology Insights, v. 3, p. 141–154, 2009.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/31046
dc.identifier.issn.pt_BR.fl_str_mv 1177-9322
identifier_str_mv CARELS, Nicolas; FRÍAS, Diego. Classifying Coding DNA with Nucleotide Statistics. Bioinformatics and Biology Insights, v. 3, p. 141–154, 2009.
1177-9322
url https://www.arca.fiocruz.br/handle/icict/31046
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Libertas Academica
publisher.none.fl_str_mv Libertas Academica
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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