Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes.

Animals Genetic Code Genome, Mitochondrial Mitochondrial Proteins / genetics Molecular Sequence Annotation / methods RNA, Messenger / genetics

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
18 11 2019
Historique:
accepted: 29 09 2019
revised: 30 08 2019
received: 06 10 2018
pubmed: 5 10 2019
medline: 8 5 2020
entrez: 5 10 2019
Statut: ppublish

Résumé

With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual annotation is becoming more and more infeasible. While it is easy to identify the approximate location of protein-coding genes within mitogenomes, the peculiar processing of mitochondrial transcripts, however, makes the determination of precise gene boundaries a surprisingly difficult problem. We have analyzed the properties of annotated start and stop codon positions in detail, and use the inferred patterns to devise a new method for predicting gene boundaries in de novo annotations. Our method benefits from empirically observed prevalances of start/stop codons and gene lengths, and considers the dependence of these features on variations of genetic codes. Albeit not being perfect, our new approach yields a drastic improvement in the accuracy of gene boundaries and upgrades the mitochondrial genome annotation server MITOS to an even more sophisticated tool for fully automatic annotation of metazoan mitochondrial genomes.

Identifiants

DOI: 10.1093/nar/gkz833 PMID: 31584075 PMC: PMC6847864
pubmed: 31584075
pii: 5580899
doi: 10.1093/nar/gkz833
pmc: PMC6847864
doi:

Substances chimiques

Mitochondrial Proteins 0
RNA, Messenger 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

10543-10552

Informations de copyright

© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Alexander Donath (A)

Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, D-53113 Bonn, Germany.

Frank Jühling (F)

Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 3 Rue Koeberlé, F-67000 Strasbourg, France.
Université de Strasbourg, 4 Rue Blaise Pascal, F-67081 Strasbourg, France.

Marwa Al-Arab (M)

Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon.

Stephan H Bernhart (SH)

Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.

Franziska Reinhardt (F)

Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.

Peter F Stadler (PF)

Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany.
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.
Fraunhofer Institut for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany.
Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA.

Martin Middendorf (M)

Swarm Intelligence and Complex Systems, Department of Computer Science, Universität Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany.

Matthias Bernt (M)

Swarm Intelligence and Complex Systems, Department of Computer Science, Universität Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany.
Helmholtz Centre for Environmental Research - UFZ, Young Investigators Group Bioinformatics and Transcriptomics Permoserstraße 15, D-04318 Leipzig, Germany.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Improved annotation of protein-coding genes...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Code génétique › Improved annotation of protein-coding genes...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome mitochondrial › Improved annotation of protein-coding genes...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines mitochondriales › Improved annotation of protein-coding genes...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › Improved annotation of protein-coding genes...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN messager › Improved annotation of protein-coding genes...