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Author Oesterhelt, Dieter ♦ Pfeiffer, Friedhelm
Source Directory of Open Access Journals (DOAJ)
Content type Text
Publisher MDPI AG
File Format PDF
Date Created 2015-06-02
Copyright Year ©2015
Language English
Subject Domain (in LCC) Q
Subject Keyword Genome annotation ♦ Halophilic archaea ♦ Science ♦ Manual curation ♦ Halobacteria ♦ Gold Standard Protein
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.
ISSN 20751729
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG ♦ Career/Technical Study
Learning Resource Type Article
Publisher Date 2015-06-01
e-ISSN 20751729
Journal Life
Volume Number 5
Issue Number 2
Page Count 18
Starting Page 1427
Ending Page 1444


Source: Directory of Open Access Journals (DOAJ)