Predicting statistical properties of open reading frames in bacterial genomes.

An analytical model based on the statistical properties of Open Reading Frames (ORFs) of eubacterial genomes such as codon composition and sequence length of all reading frames was developed. This new model predicts the average length, maximum length as well as the length distribution of the ORFs of...

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Autores principales:	Katharina Mir, Klaus Neuhaus, Siegfried Scherer, Martin Bossert, Steffen Schober
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0ade4f91d18a4724ab34f6e8400ee4a9
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id	oai:doaj.org-article:0ade4f91d18a4724ab34f6e8400ee4a9
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spelling	oai:doaj.org-article:0ade4f91d18a4724ab34f6e8400ee4a92021-11-18T07:04:24ZPredicting statistical properties of open reading frames in bacterial genomes.1932-620310.1371/journal.pone.0045103https://doaj.org/article/0ade4f91d18a4724ab34f6e8400ee4a92012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23028785/?tool=EBIhttps://doaj.org/toc/1932-6203An analytical model based on the statistical properties of Open Reading Frames (ORFs) of eubacterial genomes such as codon composition and sequence length of all reading frames was developed. This new model predicts the average length, maximum length as well as the length distribution of the ORFs of 70 species with GC contents varying between 21% and 74%. Furthermore, the number of annotated genes is predicted with high accordance. However, the ORF length distribution in the five alternative reading frames shows interesting deviations from the predicted distribution. In particular, long ORFs appear more often than expected statistically. The unexpected depletion of stop codons in these alternative open reading frames cannot completely be explained by a biased codon usage in the +1 frame. While it is unknown if the stop codon depletion has a biological function, it could be due to a protein coding capacity of alternative ORFs exerting a selection pressure which prevents the fixation of stop codon mutations. The comparison of the analytical model with bacterial genomes, therefore, leads to a hypothesis suggesting novel gene candidates which can now be investigated in subsequent wet lab experiments.Katharina MirKlaus NeuhausSiegfried SchererMartin BossertSteffen SchoberPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e45103 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Katharina Mir Klaus Neuhaus Siegfried Scherer Martin Bossert Steffen Schober Predicting statistical properties of open reading frames in bacterial genomes.
description	An analytical model based on the statistical properties of Open Reading Frames (ORFs) of eubacterial genomes such as codon composition and sequence length of all reading frames was developed. This new model predicts the average length, maximum length as well as the length distribution of the ORFs of 70 species with GC contents varying between 21% and 74%. Furthermore, the number of annotated genes is predicted with high accordance. However, the ORF length distribution in the five alternative reading frames shows interesting deviations from the predicted distribution. In particular, long ORFs appear more often than expected statistically. The unexpected depletion of stop codons in these alternative open reading frames cannot completely be explained by a biased codon usage in the +1 frame. While it is unknown if the stop codon depletion has a biological function, it could be due to a protein coding capacity of alternative ORFs exerting a selection pressure which prevents the fixation of stop codon mutations. The comparison of the analytical model with bacterial genomes, therefore, leads to a hypothesis suggesting novel gene candidates which can now be investigated in subsequent wet lab experiments.
format	article
author	Katharina Mir Klaus Neuhaus Siegfried Scherer Martin Bossert Steffen Schober
author_facet	Katharina Mir Klaus Neuhaus Siegfried Scherer Martin Bossert Steffen Schober
author_sort	Katharina Mir
title	Predicting statistical properties of open reading frames in bacterial genomes.
title_short	Predicting statistical properties of open reading frames in bacterial genomes.
title_full	Predicting statistical properties of open reading frames in bacterial genomes.
title_fullStr	Predicting statistical properties of open reading frames in bacterial genomes.
title_full_unstemmed	Predicting statistical properties of open reading frames in bacterial genomes.
title_sort	predicting statistical properties of open reading frames in bacterial genomes.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/0ade4f91d18a4724ab34f6e8400ee4a9
work_keys_str_mv	AT katharinamir predictingstatisticalpropertiesofopenreadingframesinbacterialgenomes AT klausneuhaus predictingstatisticalpropertiesofopenreadingframesinbacterialgenomes AT siegfriedscherer predictingstatisticalpropertiesofopenreadingframesinbacterialgenomes AT martinbossert predictingstatisticalpropertiesofopenreadingframesinbacterialgenomes AT steffenschober predictingstatisticalpropertiesofopenreadingframesinbacterialgenomes
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Predicting statistical properties of open reading frames in bacterial genomes.

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