Galba: genome annotation with miniprot and AUGUSTUS.

Animals Eukaryota Eukaryotic Cells Molecular Sequence Annotation Transcriptome
AUGUSTUS Gene prediction Miniprot Protein coding gene

Journal

BMC bioinformatics
ISSN: 1471-2105
Titre abrégé: BMC Bioinformatics
Pays: England
ID NLM: 100965194

Informations de publication

Date de publication:
31 Aug 2023
Historique:
received: 18 04 2023
accepted: 21 08 2023
medline: 4 9 2023
pubmed: 1 9 2023
entrez: 31 8 2023
Statut: epublish

Résumé

The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein-to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments. Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.

Sections du résumé

BACKGROUND BACKGROUND
The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes.
RESULTS RESULTS
Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein-to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments.
CONCLUSIONS CONCLUSIONS
Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.

Identifiants

DOI: 10.1186/s12859-023-05449-z PMID: 37653395 PMC: PMC10472564
pubmed: 37653395
doi: 10.1186/s12859-023-05449-z
pii: 10.1186/s12859-023-05449-z
pmc: PMC10472564
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

327

Subventions

Organisme : NHGRI NIH HHS
ID : R01 HG010040
Pays : United States
Organisme : NIH HHS
ID : R01HG010040
Pays : United States

Commentaires et corrections

Type : UpdateOf

Informations de copyright

© 2023. BioMed Central Ltd., part of Springer Nature.

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Auteurs

Tomáš Brůna (T)

U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Heng Li (H)

Department of Data Sciences, Dana-Farber Cancer Institute, Boston, 02215, MA, USA.
Department of Biomedical Informatics, Harvard Medical School, Boston, 02215, MA, USA.

Joseph Guhlin (J)

Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand.

Daniel Honsel (D)

Institute of Computer Science, University of Göttingen, 37077, Göttingen, Germany.

Steffen Herbold (S)

Faculty for Computer Science and Mathematics, University of Passau, 94032, Passau, Germany.

Mario Stanke (M)

Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489, Greifswald, Germany.

Natalia Nenasheva (N)

Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489, Greifswald, Germany.

Matthis Ebel (M)

Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489, Greifswald, Germany.

Lars Gabriel (L)

Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489, Greifswald, Germany.

Katharina J Hoff (KJ)

Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489, Greifswald, Germany. katharina.hoff@uni-greifswald.de.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Galba: genome annotation with miniprot and AUGUSTUS.
questionsmedicales.fr › Eucaryotes › Galba: genome annotation with miniprot and AUGUSTUS.
questionsmedicales.fr › Cellules › Cellules eucaryotes › Galba: genome annotation with miniprot and AUGUSTUS.
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › Galba: genome annotation with miniprot and AUGUSTUS.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Transcriptome › Galba: genome annotation with miniprot and AUGUSTUS.