Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans.

<h4>Background</h4>The C. elegans genome has been extensively annotated by the WormBase consortium that uses state of the art bioinformatics pipelines, functional genomics and manual curation approaches. As a result, the identification of novel genes in silico in this model organism is b...

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Autores principales:	Daryanaz Dargahi, David Baillie, Frederic Pio
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e29132884aad412a939a1e54b503277c
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spelling	oai:doaj.org-article:e29132884aad412a939a1e54b503277c2021-11-18T07:47:50ZBioinformatics analysis identify novel OB fold protein coding genes in C. elegans.1932-620310.1371/journal.pone.0062204https://doaj.org/article/e29132884aad412a939a1e54b503277c2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23638006/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>The C. elegans genome has been extensively annotated by the WormBase consortium that uses state of the art bioinformatics pipelines, functional genomics and manual curation approaches. As a result, the identification of novel genes in silico in this model organism is becoming more challenging requiring new approaches. The Oligonucleotide-oligosaccharide binding (OB) fold is a highly divergent protein family, in which protein sequences, in spite of having the same fold, share very little sequence identity (5-25%). Therefore, evidence from sequence-based annotation may not be sufficient to identify all the members of this family. In C. elegans, the number of OB-fold proteins reported is remarkably low (n=46) compared to other evolutionary-related eukaryotes, such as yeast S. cerevisiae (n=344) or fruit fly D. melanogaster (n=84). Gene loss during evolution or differences in the level of annotation for this protein family, may explain these discrepancies.<h4>Methodology/principal findings</h4>This study examines the possibility that novel OB-fold coding genes exist in the worm. We developed a bioinformatics approach that uses the most sensitive sequence-sequence, sequence-profile and profile-profile similarity search methods followed by 3D-structure prediction as a filtering step to eliminate false positive candidate sequences. We have predicted 18 coding genes containing the OB-fold that have remarkably partially been characterized in C. elegans.<h4>Conclusions/significance</h4>This study raises the possibility that the annotation of highly divergent protein fold families can be improved in C. elegans. Similar strategies could be implemented for large scale analysis by the WormBase consortium when novel versions of the genome sequence of C. elegans, or other evolutionary related species are being released. This approach is of general interest to the scientific community since it can be used to annotate any genome.Daryanaz DargahiDavid BaillieFrederic PioPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 4, p e62204 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Daryanaz Dargahi David Baillie Frederic Pio Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans.
description	<h4>Background</h4>The C. elegans genome has been extensively annotated by the WormBase consortium that uses state of the art bioinformatics pipelines, functional genomics and manual curation approaches. As a result, the identification of novel genes in silico in this model organism is becoming more challenging requiring new approaches. The Oligonucleotide-oligosaccharide binding (OB) fold is a highly divergent protein family, in which protein sequences, in spite of having the same fold, share very little sequence identity (5-25%). Therefore, evidence from sequence-based annotation may not be sufficient to identify all the members of this family. In C. elegans, the number of OB-fold proteins reported is remarkably low (n=46) compared to other evolutionary-related eukaryotes, such as yeast S. cerevisiae (n=344) or fruit fly D. melanogaster (n=84). Gene loss during evolution or differences in the level of annotation for this protein family, may explain these discrepancies.<h4>Methodology/principal findings</h4>This study examines the possibility that novel OB-fold coding genes exist in the worm. We developed a bioinformatics approach that uses the most sensitive sequence-sequence, sequence-profile and profile-profile similarity search methods followed by 3D-structure prediction as a filtering step to eliminate false positive candidate sequences. We have predicted 18 coding genes containing the OB-fold that have remarkably partially been characterized in C. elegans.<h4>Conclusions/significance</h4>This study raises the possibility that the annotation of highly divergent protein fold families can be improved in C. elegans. Similar strategies could be implemented for large scale analysis by the WormBase consortium when novel versions of the genome sequence of C. elegans, or other evolutionary related species are being released. This approach is of general interest to the scientific community since it can be used to annotate any genome.
format	article
author	Daryanaz Dargahi David Baillie Frederic Pio
author_facet	Daryanaz Dargahi David Baillie Frederic Pio
author_sort	Daryanaz Dargahi
title	Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans.
title_short	Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans.
title_full	Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans.
title_fullStr	Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans.
title_full_unstemmed	Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans.
title_sort	bioinformatics analysis identify novel ob fold protein coding genes in c. elegans.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/e29132884aad412a939a1e54b503277c
work_keys_str_mv	AT daryanazdargahi bioinformaticsanalysisidentifynovelobfoldproteincodinggenesincelegans AT davidbaillie bioinformaticsanalysisidentifynovelobfoldproteincodinggenesincelegans AT fredericpio bioinformaticsanalysisidentifynovelobfoldproteincodinggenesincelegans
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Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans.

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