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Life 2015, 5(2), 1427-1444; doi:10.3390/life5021427

A Manual Curation Strategy to Improve Genome Annotation: Application to a Set of Haloarchael Genomes

Department of Membrane Biochemistry, Max-Planck-Institute of Biochemisty, Am Klopferspitz 18, Martinsried 82152, Germany
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Author to whom correspondence should be addressed.
Academic Editors: Hans-Peter Klenk, Michael W. W. Adams and Roger A. Garrett
Received: 2 April 2015 / Revised: 22 May 2015 / Accepted: 25 May 2015 / Published: 2 June 2015
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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Abstract

Genome annotation errors are a persistent problem that impede research in the biosciences. A manual curation effort is described that attempts to produce high-quality genome annotations for a set of haloarchaeal genomes (Halobacterium salinarum and Hbt. hubeiense, Haloferax volcanii and Hfx. mediterranei, Natronomonas pharaonis and Nmn. moolapensis, Haloquadratum walsbyi strains HBSQ001 and C23, Natrialba magadii, Haloarcula marismortui and Har. hispanica, and Halohasta litchfieldiae). Genomes are checked for missing genes, start codon misassignments, and disrupted genes. Assignments of a specific function are preferably based on experimentally characterized homologs (Gold Standard Proteins). To avoid overannotation, which is a major source of database errors, we restrict annotation to only general function assignments when support for a specific substrate assignment is insufficient. This strategy results in annotations that are resistant to the plethora of errors that compromise public databases. Annotation consistency is rigorously validated for ortholog pairs from the genomes surveyed. The annotation is regularly crosschecked against the UniProt database to further improve annotations and increase the level of standardization. Enhanced genome annotations are submitted to public databases (EMBL/GenBank, UniProt), to the benefit of the scientific community. The enhanced annotations are also publically available via HaloLex. View Full-Text
Keywords: genome annotation; Gold Standard Protein; Halobacteria; halophilic archaea; manual curation genome annotation; Gold Standard Protein; Halobacteria; halophilic archaea; manual curation
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Pfeiffer, F.; Oesterhelt, D. A Manual Curation Strategy to Improve Genome Annotation: Application to a Set of Haloarchael Genomes. Life 2015, 5, 1427-1444.

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