title: Evaluation of three automated genome annotations for Halorhabdus utahensis.
abstract: Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited in databases such as NCBI and used to validate subsequent annotation errors. We submitted the genome sequence of halophilic archaeon Halorhabdus utahensis to be analyzed by three genome annotation services. We have examined the output from each service in a variety of ways in order to compare the methodology and effectiveness of the annotations, as well as to explore the genes, pathways, and physiology of the previously unannotated genome. The annotation services differ considerably in gene calls, features, and ease of use. We had to manually identify the origin of replication and the species-specific consensus ribosome-binding site. Additionally, we conducted laboratory experiments to test H. utahensis growth and enzyme activity. Current annotation practices need to improve in order to more accurately reflect a genome's biological potential. We make specific recommendations that could improve the quality of microbial annotation projects.
authors.affiliation: Department of Biology, Davidson College, Davidson, NC, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Bakke
authors.forename: Nick
authors.initials: N
authors.lastname: Carney
authors.forename: Will
authors.initials: W
authors.lastname: Deloache
authors.forename: Mary
authors.initials: M
authors.lastname: Gearing
authors.forename: Kjeld
authors.initials: K
authors.lastname: Ingvorsen
authors.forename: Matt
authors.initials: M
authors.lastname: Lotz
authors.forename: Jay
authors.initials: J
authors.lastname: McNair
authors.forename: Pallavi
authors.initials: P
authors.lastname: Penumetcha
authors.forename: Samantha
authors.initials: S
authors.lastname: Simpson
authors.forename: Laura
authors.initials: L
authors.lastname: Voss
authors.forename: Max
authors.initials: M
authors.lastname: Win
authors.forename: Laurie J
authors.initials: LJ
authors.lastname: Heyer
authors.forename: A Malcolm
authors.initials: AM
authors.lastname: Campbell
mesh_terms: D020745:Genome, Archaeal; D006216:Halobacteriaceae / Q000235:genetics*; D007438:Introns; D012343:RNA, Transfer / Q000235:genetics; D018741:Replication Origin
chemical_list: D012343:RNA, Transfer