{"doi":"10.1371/journal.pone.0006291","title":"Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis","abstract":null,"journal":"PLoS ONE","year":2009,"id":47105,"datarank":3.9009146774653165,"base_score":4.3694478524670215,"endowment":4.3694478524670215,"self_citation_contribution":0.6554171778700533,"citation_network_contribution":3.2454974995952632,"self_endowment_contribution":0.6554171778700533,"citer_contribution":3.2454974995952632,"corpus_percentile":null,"corpus_rank":null,"citation_count":78,"citer_count":78,"citers_with_citation_signal":60,"citers_with_endowment":60,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":217508,"name":"Nick Carney","orcid":null,"position":1,"is_corresponding":false},{"id":217509,"name":"Will DeLoache","orcid":null,"position":2,"is_corresponding":false},{"id":217510,"name":"Mary Gearing","orcid":null,"position":3,"is_corresponding":false},{"id":217511,"name":"Kjeld Ingvorsen","orcid":null,"position":4,"is_corresponding":false},{"id":217512,"name":"Matt Lotz","orcid":null,"position":5,"is_corresponding":false},{"id":217513,"name":"Jay McNair","orcid":null,"position":6,"is_corresponding":false},{"id":217514,"name":"Pallavi Penumetcha","orcid":null,"position":7,"is_corresponding":false},{"id":217515,"name":"Samantha Simpson","orcid":null,"position":8,"is_corresponding":false},{"id":217516,"name":"Laura Voss","orcid":null,"position":9,"is_corresponding":false},{"id":217517,"name":"Max Win","orcid":null,"position":10,"is_corresponding":false},{"id":217518,"name":"Laurie J. Heyer","orcid":null,"position":11,"is_corresponding":false},{"id":217519,"name":"A. Malcolm Campbell","orcid":null,"position":12,"is_corresponding":false},{"id":217507,"name":"Peter Bakke","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"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.","is_dataset_classified":null,"base_score":4.3694478524670215,"endowment":4.3694478524670215,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19617911","pmcid":"PMC2707008","openalex_id":"https://openalex.org/W2043778888","authors":[],"funders":[{"funder_name":"Howard Hughes Medical Institute","grant_id":"52006292","title":null},{"funder_name":"Howard Hughes Medical Institute","grant_id":"52005120","title":null},{"funder_name":"National Science Foundation","grant_id":"0733952","title":"Collaborative Research: UBM Group: Synthetic Biology Research for Undergraduates (SyBR-U)"}],"total_grants":3,"fwci":3.6506,"citation_percentile":0.9376662,"influential_citations":2,"citation_trend":[{"year":2012,"count":9},{"year":2013,"count":10},{"year":2014,"count":7},{"year":2015,"count":14},{"year":2016,"count":2},{"year":2017,"count":4},{"year":2018,"count":1},{"year":2019,"count":3},{"year":2020,"count":2},{"year":2021,"count":1},{"year":2023,"count":1},{"year":2024,"count":2},{"year":2025,"count":1}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0006291&type=printable","host_type":"journal"},{"url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0006291&type=printable","host_type":"GOLD"},{"url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0006291&type=printable","host_type":"publisher"},{"url":"https://doi.org/10.1371/journal.pone.0006291","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/19617911","host_type":"repository"},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.357.8843","host_type":""},{"url":"https://doaj.org/article/44d5eb85f76740618a0b7da1e3e59285","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2707008","host_type":"repository"},{"url":"https://pure.au.dk/portal/en/publications/76d8b340-a1d6-11de-a092-000ea68e967b","host_type":""},{"url":"https://europepmc.org/articles/PMC2707008","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC2707008?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1371/journal.pone.0006291","host_type":""},{"url":"https://dx.doi.org/10.1371/journal.pone.0006291","host_type":""}],"fields_of_study":["Genomics and Phylogenetic Studies","Insect symbiosis and bacterial influences","Entomopathogenic Microorganisms in Pest Control","Biology","Medicine","Environmental Science","Computer Science","0301 basic medicine","0303 health sciences","03 medical and health sciences","Genome, Archaeal","Halobacteriaceae","Introns","RNA, Transfer","Replication Origin"],"mesh_terms":["Halobacteriaceae","Introns","RNA, Transfer","Replication Origin","Genome, Archaeal"],"keywords":["Annotation","Genome","Genome project","Gene Annotation","Computational biology","DNA sequencing","Computer science","Biology","Gene prediction","Gene","Bioinformatics","Genetics","Halobacteriaceae","RNA, Transfer","Genome, Archaeal","Science","Q","R","Medicine","Replication Origin","Introns","Research Article"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-17T01:40:50.423162Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}