Assessment of genome annotation using gene function similarity within the gene neighborhood

Jun, Se-Ran; Nookaew, Intawat; Hauser, Loren; Gorin, Andrey

doi:10.1186/s12859-017-1761-2

Title: Assessment of genome annotation using gene function similarity within the gene neighborhood

Journal Article · 19 July 2017 · BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-017-1761-2 · OSTI ID:1626764

^[1]; Nookaew, Intawat ^[1]; Hauser, Loren ^[2]; Gorin, Andrey ^[2]

Univ. of Arkansas for Medical Sciences, Little Rock, AR (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Functional annotation of bacterial genomes is an obligatory and crucially important step of information processing from the genome sequences into cellular mechanisms. However, there is a lack of computational methods to evaluate the quality of functional assignments. Results: We developed a genome-scale model that assigns Bayesian probability to each gene utilizing a known property of functional similarity between neighboring genes in bacteria. Conclusions: Our model clearly distinguished true annotation from random annotation with Bayesian annotation probability >0.95. Our model will provide a useful guide to quantitatively evaluate functional annotation methods and to detect gene sets with reliable annotations.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1626764

Journal Information:: BMC Bioinformatics, Vol. 18, Issue 1; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments Monk, J. M.; Charusanti, P.; Aziz, R. K. Proceedings of the National Academy of Sciences, Vol. 110, Issue 50 https://doi.org/10.1073/pnas.1307797110	journal	November 2013
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Data, information, knowledge and principle: back to metabolism in KEGG Kanehisa, Minoru; Goto, Susumu; Sato, Yoko Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1076	journal	November 2013
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Quality scores for 32,000 genomes Land, Miriam L.; Hyatt, Doug; Jun, Se-Ran Standards in Genomic Sciences, Vol. 9, Issue 1 https://doi.org/10.1186/1944-3277-9-20	journal	December 2014
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Cited By (2)

Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa Amoako, Daniel Gyamfi; Somboro, Anou M.; Abia, Akebe Luther King Pathogens, Vol. 8, Issue 4 https://doi.org/10.3390/pathogens8040166	journal	September 2019
Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa Amoako, Daniel Gyamfi; Somboro, Anou M.; Abia, Akebe Luther King Pathogens, Vol. 8, Issue 4 https://doi.org/10.3390/pathogens8040166	journal	September 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Mathematical & Computational Biology
Genome Functional Annotation
Gene Function Similarity
Gene neighborhood
Bayesian Probability

Assessment of genome annotation using gene function similarity within the gene neighborhood Jun, Se-Ran; Nookaew, Intawat; Hauser, Loren https://doi.org/10.6084/m9.figshare.c.3831253 The current record is supplemented by this collection	collection	January 2017
Assessment of genome annotation using gene function similarity within the gene neighborhood Jun, Se-Ran; Nookaew, Intawat; Hauser, Loren https://doi.org/10.6084/m9.figshare.c.3831253.v1 The current record is supplemented by this collection	collection	January 2017
Additional file 1: of Assessment of genome annotation using gene function similarity within the gene neighborhood Jun, Se-Ran; Nookaew, Intawat; Hauser, Loren https://doi.org/10.6084/m9.figshare.c.3831253_d1 The current record is supplemented by this text	text	January 2017
Additional file 1: of Assessment of genome annotation using gene function similarity within the gene neighborhood Jun, Se-Ran; Nookaew, Intawat; Hauser, Loren https://doi.org/10.6084/m9.figshare.c.3831253_d1.v1 The current record is supplemented by this text	text	January 2017
Additional file 2: of Assessment of genome annotation using gene function similarity within the gene neighborhood Jun, Se-Ran; Nookaew, Intawat; Hauser, Loren https://doi.org/10.6084/m9.figshare.c.3831253_d2 The current record is supplemented by this dataset	dataset	January 2017
Additional file 2: of Assessment of genome annotation using gene function similarity within the gene neighborhood Jun, Se-Ran; Nookaew, Intawat; Hauser, Loren https://doi.org/10.6084/m9.figshare.c.3831253_d2.v1 The current record is supplemented by this dataset	dataset	January 2017