Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis
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{"title"=>"Evaluation of three automated genome annotations for Halorhabdus utahensis", "type"=>"journal", "authors"=>[{"first_name"=>"Peter", "last_name"=>"Bakke", "scopus_author_id"=>"28367479200"}, {"first_name"=>"Nick", "last_name"=>"Carney", "scopus_author_id"=>"28367510900"}, {"first_name"=>"Will", "last_name"=>"DeLoache", "scopus_author_id"=>"36941416100"}, {"first_name"=>"Mary", "last_name"=>"Gearing", "scopus_author_id"=>"28367573700"}, {"first_name"=>"Kjeld", "last_name"=>"Ingvorsen", "scopus_author_id"=>"6603794028"}, {"first_name"=>"Matt", "last_name"=>"Lotz", "scopus_author_id"=>"28367699400"}, {"first_name"=>"Jay", "last_name"=>"McNair", "scopus_author_id"=>"28367826200"}, {"first_name"=>"Pallavi", "last_name"=>"Penumetcha", "scopus_author_id"=>"57199519581"}, {"first_name"=>"Samantha", "last_name"=>"Simpson", "scopus_author_id"=>"57196937910"}, {"first_name"=>"Laura", "last_name"=>"Voss", "scopus_author_id"=>"28367942500"}, {"first_name"=>"Max", "last_name"=>"Win", "scopus_author_id"=>"28368085300"}, {"first_name"=>"Laurie J.", "last_name"=>"Heyer", "scopus_author_id"=>"6602142236"}, {"first_name"=>"A. Malcolm", "last_name"=>"Campbell", "scopus_author_id"=>"55445771400"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"19617911", "doi"=>"10.1371/journal.pone.0006291", "sgr"=>"67651091927", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-67651091927", "issn"=>"19326203", "pui"=>"354972153"}, "id"=>"6e7919f9-4a93-34e2-a34b-21944ee6e99f", "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.", "link"=>"http://www.mendeley.com/research/evaluation-three-automated-genome-annotations-halorhabdus-utahensis", "reader_count"=>104, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Librarian"=>1, "Researcher"=>37, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>1, "Student > Master"=>16, "Other"=>3, "Student > Bachelor"=>7, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Librarian"=>1, "Researcher"=>37, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>1, "Student > Master"=>16, "Other"=>3, "Student > Bachelor"=>7, "Professor"=>5}, "reader_count_by_subject_area"=>{"Engineering"=>3, "Unspecified"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>84, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Computer Science"=>5}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>84}, "Computer Science"=>{"Computer Science"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>6, "United Kingdom"=>2, "Spain"=>1, "India"=>1, "Russia"=>1, "Greece"=>1, "Saudi Arabia"=>1, "Sweden"=>1, "Denmark"=>1, "Brazil"=>4, "Mexico"=>1, "Chile"=>2, "Estonia"=>1}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/892037"], "description"=>"<p>Mean, median, minimum, and maximum gene lengths of the total predicted coding regions illustrate differences in gene calls between the annotations.</p>", "links"=>[], "tags"=>["descriptive"], "article_id"=>562477, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.t002", "stats"=>{"downloads"=>7, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_descriptive_statistics_/562477", "title"=>"Comparison of descriptive statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 05:23:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/891723"], "description"=>"<p>Illustrates average gene length for two categories. Red bars represent the average length of genes from each annotation that have distinct stop codons. Blue bars represent the average length of genes that have a common stop codon across the three annotations.</p>", "links"=>[], "tags"=>["genetics and genomics", "computational biology/comparative sequence analysis", "computational biology/genomics", "genetics and genomics/bioinformatics", "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics", "molecular biology/bioinformatics", "molecular biology/molecular evolution"], "article_id"=>562156, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.g005", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_average_gene_length_/562156", "title"=>"Comparison of average gene length.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:21:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/891970"], "description"=>"<p>Hypothetical comparison of start sites from multiple annotations, combined with species-specific RBS data. Start #2 would be the most likely start codon based on RBS spacing.</p>", "links"=>[], "tags"=>["genetics and genomics", "computational biology/comparative sequence analysis", "computational biology/genomics", "genetics and genomics/bioinformatics", "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics", "molecular biology/bioinformatics", "molecular biology/molecular evolution"], "article_id"=>562410, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.g007", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Potential_comparison_tool_/562410", "title"=>"Potential comparison tool.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:23:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/891473"], "description"=>"<p>Histograms displaying gene length illustrate similarities and differences between annotations. (A) Frequency of genes called by IMG at different lengths. (B) Frequency of genes called by RAST at different lengths. (C) Frequency of genes called by JCVI at different lengths. JCVI has a higher frequency of short genes called than IMG or RAST.</p>", "links"=>[], "tags"=>["genetics and genomics", "computational biology/comparative sequence analysis", "computational biology/genomics", "genetics and genomics/bioinformatics", "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics", "molecular biology/bioinformatics", "molecular biology/molecular evolution"], "article_id"=>561901, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_gene_length_frequencies_/561901", "title"=>"Comparison of gene length frequencies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:20:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/892101"], "description"=>"<p>Analysis of predicted protein coding genes displays incidence of ATG and alternative start codons for each annotation. RAST has a greater tendency to call genes with alternative start codons than the other annotation services.</p>", "links"=>[], "tags"=>["genetics and genomics", "computational biology/comparative sequence analysis", "computational biology/genomics", "genetics and genomics/bioinformatics", "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics", "molecular biology/bioinformatics", "molecular biology/molecular evolution"], "article_id"=>562536, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.t003", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_start_codons_/562536", "title"=>"Comparison of start codons.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 05:23:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/891072"], "description"=>"<p>Histogram displaying the frequency of the consensus RBS at varying spacer lengths. Spacer length refers to the number of base pairs between the 3′ end of the RBS and the 5′ end of the start codon for each gene. The consensus RBS generally lies between 4 and 8 base pairs upstream of the start codon.</p>", "links"=>[], "tags"=>["rbs", "spacer"], "article_id"=>561507, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.g001", "stats"=>{"downloads"=>2, "page_views"=>41, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_RBS_spacer_lengths_/561507", "title"=>"Comparison of RBS spacer lengths.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:18:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/892273"], "description"=>"<p>The annotation services use different names to identify the same protein.</p>", "links"=>[], "tags"=>["genetics and genomics", "computational biology/comparative sequence analysis", "computational biology/genomics", "genetics and genomics/bioinformatics", "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics", "molecular biology/bioinformatics", "molecular biology/molecular evolution"], "article_id"=>562711, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.t005", "stats"=>{"downloads"=>3, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_gene_names_/562711", "title"=>"Comparison of gene names.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 05:24:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/891844"], "description"=>"<p>Diagram based on RAST's KEGG pathway map displays present and absent enzymes for <i>H. utahensis</i>. Green boxes indicate that the enzyme was predicted by RAST and displayed in the KEGG map. Yellow boxes designate enzymes that were called by RAST but had not been added to the KEGG map. Red boxes mark enzymes that were listed as absent and could not be located in the <i>H. utahensis</i> genome.</p>", "links"=>[], "tags"=>["genetics and genomics", "computational biology/comparative sequence analysis", "computational biology/genomics", "genetics and genomics/bioinformatics", "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics", "molecular biology/bioinformatics", "molecular biology/molecular evolution"], "article_id"=>562282, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.g006", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Glycolysis_gluconeogenesis_pathway_/562282", "title"=>"Glycolysis/gluconeogenesis pathway.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:22:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/892176"], "description"=>"<p>We incubated <i>H. utahensis</i> for seven days in GSL-2 medium with various macromolecular substrates. The topmost row lists the macromolecular substrates used as carbon sources. The first nine entries in the leftmost column indicate the substrates used for enzyme assays. Plus signs denote the level of activity, ranging in order of lowest to highest from 0 to +++.</p>", "links"=>[], "tags"=>["wet-lab"], "article_id"=>562620, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.t006", "stats"=>{"downloads"=>4, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_wet_lab_results_/562620", "title"=>"Summary of wet-lab results.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 05:24:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/892225"], "description"=>"<p>Examination of an individual gene displays tendencies of the annotation services. RAST identifies GTG as the start codon for the gene, while IMG and JCVI select two ATG codons at different locations. Predicted start codon affects gene length.</p>", "links"=>[], "tags"=>["putative", "glycoside", "hydrolase"], "article_id"=>562666, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_putative_glycoside_hydrolase_start_sites_/562666", "title"=>"Comparison of putative glycoside hydrolase start sites.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 05:24:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/892136"], "description"=>"<p>Review of predicted coding regions for ribosomal RNA for each annotation service shows that IMG and RAST have identical calls, while JCVI fails to call 23s rRNA and predicts different start and stop sites.</p>", "links"=>[], "tags"=>["rrna"], "article_id"=>562583, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.t001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_rRNA_calls_/562583", "title"=>"Comparison of rRNA calls.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 05:24:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/891612"], "description"=>"<p>(A) The diagram to the left shows the number of predicted protein coding genes that share stop sites with the other annotations. Overlapping regions indicate genes having same stop site between annotations. (B) The diagram to the right shows the number of predicted protein coding genes that share start site and stop site with the other annotations. Overlapping regions indicate genes having exact matches between annotations.</p>", "links"=>[], "tags"=>["diagrams"], "article_id"=>562058, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.g004", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Venn_diagrams_of_gene_predictions_/562058", "title"=>"Venn diagrams of gene predictions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:21:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/891233"], "description"=>"<p>Circular display of the largest contig of the <i>H. utahensis</i> genome sequence. The contig begins at the top and wraps clockwise. The red bars illustrate the location of ORC/Cdc6 orthologs. The ORC/Cdc6 gene numbered 3 lies near the origin of replication, at 2,327,225 base pairs.</p>", "links"=>[], "tags"=>["contig"], "article_id"=>561675, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Infectious Diseases"], "users"=>["Peter Bakke", "Nick Carney", "Will DeLoache", "Mary Gearing", "Kjeld Ingvorsen", "Matt Lotz", "Jay McNair", "Pallavi Penumetcha", "Samantha Simpson", "Laura Voss", "Max Win", "Laurie J. Heyer", "A. Malcolm Campbell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006291.g002", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_H_utahensis_primary_contig_and_ORC_Cdc6_genes_/561675", "title"=>"<i>H. utahensis</i> primary contig and ORC/Cdc6 genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:19:19"}

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  • {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"11"}
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Relative Metric

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