Measuring Global Credibility with Application to Local Sequence Alignment
Publication Date
May 16, 2008
Journal
PLOS Computational Biology
Authors
Bobbie Jo M. Webb Robertson, Lee Ann Mc Cue & Charles E. Lawrence
Volume
4
Issue
5
Pages
e1000077
DOI
http://doi.org/10.1371/journal.pcbi.1000077
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1000077
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/18464927
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367447
Europe PMC
http://europepmc.org/abstract/MED/18464927
Web of Science
000256866400015
Scopus
44949258055
Mendeley
http://www.mendeley.com/research/measuring-global-credibility-application-local-sequence-alignment
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CiteULike | Further Information

Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/931253"], "description"=>"<p>In (A) the centroid and optimal alignments are similar and represent the distribution well, but in (B) and (C), despite a similar centroid and optimal alignment, neither represent the overall alignment distribution. In (D) it is observed that the centroid and optimal deviate significantly from each other, and that the centroid is a much better representation of the alignment space.</p>", "links"=>[], "tags"=>["distances", "sampled", "alignments", "ec"], "article_id"=>601698, "categories"=>["Mathematics", "Molecular Biology", "Virology"], "users"=>["Bobbie-Jo M. Webb-Robertson", "Lee Ann McCue", "Charles E. Lawrence"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000077.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Histograms_of_the_distances_of_the_sampled_alignments_from_the_EC_and_MS_/601698", "title"=>"Histograms of the distances of the sampled alignments from the EC and MS.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-16 00:28:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/931327"], "description"=>"<p>The four example alignment <i>ND</i> distributions displayed in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000077#pcbi-1000077-g004\" target=\"_blank\">Figure 4</a> are indicated by a letter next to the corresponding symbol.</p>", "links"=>[], "tags"=>["ec", "ms", "120", "pairwise", "alignments", "comparisons"], "article_id"=>601770, "categories"=>["Mathematics", "Molecular Biology", "Virology"], "users"=>["Bobbie-Jo M. Webb-Robertson", "Lee Ann McCue", "Charles E. Lawrence"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000077.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plot_of_ND_95_values_for_the_EC_versus_the_MS_of_120_pairwise_sequence_alignments_24_comparisons_for_each_of_the_five_species_in_the_legend_to_SMR4_/601770", "title"=>"Plot of <i>ND</i><sub>95</sub> values for the EC versus the MS of 120 pairwise sequence alignments (24 comparisons for each of the five species in the legend to SMR4).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-16 00:29:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/931203"], "description"=>"<p>The <i>ND</i><sub>95</sub> values associated with the 20 highly conserved gene sequences are represented as green circles. The sequence alignments that represent alignment of random, un-related, sequences are represented as black triangles. In blue squares are the <i>ND</i><sub>95</sub> values for the intergenic sequences upstream of the coding genes. The four example alignment <i>ND</i> distributions displayed in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000077#pcbi-1000077-g002\" target=\"_blank\">Figure 2</a> are indicated by a letter next to the corresponding square.</p>", "links"=>[], "tags"=>["ec", "ms", "20", "pairwise"], "article_id"=>601646, "categories"=>["Mathematics", "Molecular Biology", "Virology"], "users"=>["Bobbie-Jo M. Webb-Robertson", "Lee Ann McCue", "Charles E. Lawrence"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000077.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plot_of_ND_95_values_for_the_EC_versus_the_MS_of_20_pairwise_sequence_alignments_/601646", "title"=>"Plot of <i>ND</i><sub>95</sub> values for the EC versus the MS of 20 pairwise sequence alignments.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-16 00:27:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/931469"], "description"=>"<p>(A) Alignment distribution for the regions upstream of the orthologous genes SMR4_0576 and CN32_3301 and (B) alignment distribution for the orthologous regions upstream of the arginine decarboxylase (speA) genes SMR4_1557 and CN32_1647.</p>", "links"=>[], "tags"=>["distances", "sampled", "alignments", "ec", "ms", "intergenic", "regions", "upstream", "orthologous", "genes", "smr4"], "article_id"=>601906, "categories"=>["Mathematics", "Molecular Biology", "Virology"], "users"=>["Bobbie-Jo M. Webb-Robertson", "Lee Ann McCue", "Charles E. Lawrence"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000077.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Histograms_of_the_distances_of_the_sampled_alignments_from_the_EC_and_MS_for_the_intergenic_regions_upstream_of_orthologous_genes_from_SMR4_and_CN32_/601906", "title"=>"Histograms of the distances of the sampled alignments from the EC and MS for the intergenic regions upstream of orthologous genes from SMR4 and CN32.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-16 00:31:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/931685"], "description"=>"<p>Gene, <i>ND</i><sub>95</sub>, P-Quantile information on examples highlighted in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000077#pcbi-1000077-g001\" target=\"_blank\">Figures 1</a> and <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000077#pcbi-1000077-g002\" target=\"_blank\">2</a>.</p>", "links"=>[], "tags"=>["p-quantile", "examples", "highlighted"], "article_id"=>602131, "categories"=>["Mathematics", "Molecular Biology", "Virology"], "users"=>["Bobbie-Jo M. Webb-Robertson", "Lee Ann McCue", "Charles E. Lawrence"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000077.t001", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_ND_95_P_Quantile_information_on_examples_highlighted_in_Figures_1_and_2_/602131", "title"=>"Gene, <i>ND</i><sub>95</sub>, P-Quantile information on examples highlighted in Figures 1 and 2.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-16 00:35:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/458951"], "description"=>"<div><p>Computational biology is replete with high-dimensional (high-D) discrete prediction and inference problems, including sequence alignment, RNA structure prediction, phylogenetic inference, motif finding, prediction of pathways, and model selection problems in statistical genetics. Even though prediction and inference in these settings are uncertain, little attention has been focused on the development of global measures of uncertainty. Regardless of the procedure employed to produce a prediction, when a procedure delivers a single answer, that answer is a point estimate selected from the solution ensemble, the set of all possible solutions. For high-D discrete space, these ensembles are immense, and thus there is considerable uncertainty. We recommend the use of Bayesian credibility limits to describe this uncertainty, where a (1−<em>α</em>)%, 0≤<em>α</em>≤1, credibility limit is the minimum Hamming distance radius of a hyper-sphere containing (1−<em>α</em>)% of the posterior distribution. Because sequence alignment is arguably the most extensively used procedure in computational biology, we employ it here to make these general concepts more concrete. The maximum similarity estimator (i.e., the alignment that maximizes the likelihood) and the centroid estimator (i.e., the alignment that minimizes the mean Hamming distance from the posterior weighted ensemble of alignments) are used to demonstrate the application of Bayesian credibility limits to alignment estimators. Application of Bayesian credibility limits to the alignment of 20 human/rodent orthologous sequence pairs and 125 orthologous sequence pairs from six <em>Shewanella</em> species shows that credibility limits of the alignments of promoter sequences of these species vary widely, and that centroid alignments dependably have tighter credibility limits than traditional maximum similarity alignments.</p></div>", "links"=>[], "tags"=>["measuring", "alignment"], "article_id"=>150423, "categories"=>["Mathematics", "Molecular Biology", "Cancer"], "users"=>["Bobbie-Jo M. Webb-Robertson", "Lee Ann McCue", "Charles E. Lawrence"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000077", "stats"=>{"downloads"=>6, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Measuring_Global_Credibility_with_Application_to_Local_Sequence_Alignment/150423", "title"=>"Measuring Global Credibility with Application to Local Sequence Alignment", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-16 00:07:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/931375"], "description"=>"<p>SMR4_0576 alignment distribution with its orthologous sequence from (A) SONE, (B) CN32, (C) SPV4, and (D) DENI.</p>", "links"=>[], "tags"=>["distances", "sampled", "alignments", "ec", "ms", "intergenic", "regions", "upstream"], "article_id"=>601816, "categories"=>["Mathematics", "Molecular Biology", "Virology"], "users"=>["Bobbie-Jo M. Webb-Robertson", "Lee Ann McCue", "Charles E. Lawrence"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000077.g004", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Histograms_of_the_distances_of_the_sampled_alignments_from_the_EC_and_MS_for_the_intergenic_regions_upstream_of_the_gene_SMR4_0576_/601816", "title"=>"Histograms of the distances of the sampled alignments from the EC and MS for the intergenic regions upstream of the gene SMR4_0576.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-16 00:30:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/931630"], "description"=>"<p>This scatter plot demonstrates that probability-based alignments (e.g., EC) typically have higher similarity with structural alignments than MS alignments.</p>", "links"=>[], "tags"=>["squared", "deviation", "ec", "ms", "x-ray"], "article_id"=>602073, "categories"=>["Mathematics", "Molecular Biology", "Virology"], "users"=>["Bobbie-Jo M. Webb-Robertson", "Lee Ann McCue", "Charles E. Lawrence"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000077.g007", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Root_mean_squared_r_m_s_deviation_between_the_EC_and_MS_for_X_ray_crystal_structure_data_26_/602073", "title"=>"Root mean squared (r.m.s) deviation between the EC and MS for X-ray crystal structure data [26].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-16 00:34:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/931529"], "description"=>"<p>Sequence indices are given on the left and the color gradient associated with aligned residue probabilities is given on the right. Sequence regions that have no aligned pairs with a probability greater than 0.5 are ignored by the alignment, grayed out, and aligned with a dot to differentiate these from insertion/deletion events that utilize a dash.</p>", "links"=>[], "tags"=>["alignment"], "article_id"=>601981, "categories"=>["Mathematics", "Molecular Biology", "Virology"], "users"=>["Bobbie-Jo M. Webb-Robertson", "Lee Ann McCue", "Charles E. Lawrence"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000077.g006", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heat_map_alignment_representation_of_the_EC_/601981", "title"=>"Heat-map alignment representation of the EC.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-16 00:33:01"}

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