SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework
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{"title"=>"Simulfold: Simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework", "type"=>"journal", "authors"=>[{"first_name"=>"Irmtraud M.", "last_name"=>"Meyer", "scopus_author_id"=>"20735018600"}, {"first_name"=>"István", "last_name"=>"Miklós", "scopus_author_id"=>"7003749674"}], "year"=>2007, "source"=>"PLoS Computational Biology", "identifiers"=>{"isbn"=>"1553-7358 (Electronic)", "sgr"=>"34548443728", "doi"=>"10.1371/journal.pcbi.0030149", "pui"=>"47358054", "scopus"=>"2-s2.0-34548443728", "issn"=>"1553734X", "pmid"=>"17696604"}, "id"=>"4e4eeb96-8510-37d2-8e0a-c9d6ae13e3a2", "abstract"=>"Computational methods for predicting evolutionarily conserved rather than thermodynamic RNA structures have recently attracted increased interest. These methods are indispensable not only for elucidating the regulatory roles of known RNA transcripts, but also for predicting RNA genes. It has been notoriously difficult to devise them to make the best use of the available data and to predict high-quality RNA structures that may also contain pseudoknots. We introduce a novel theoretical framework for co-estimating an RNA secondary structure including pseudoknots, a multiple sequence alignment, and an evolutionary tree, given several RNA input sequences. We also present an implementation of the framework in a new computer program, called SimulFold, which employs a Bayesian Markov chain Monte Carlo method to sample from the joint posterior distribution of RNA structures, alignments, and trees. We use the new framework to predict RNA structures, and comprehensively evaluate the quality of our predictions by comparing our results to those of several other programs. We also present preliminary data that show SimulFold's potential as an alignment and phylogeny prediction method. SimulFold overcomes many conceptual limitations that current RNA structure prediction methods face, introduces several new theoretical techniques, and generates high-quality predictions of conserved RNA structures that may include pseudoknots. It is thus likely to have a strong impact, both on the field of RNA structure prediction and on a wide range of data analyses.", "link"=>"http://www.mendeley.com/research/simulfold-simultaneously-inferring-rna-structures-including-pseudoknots-alignments-trees-using-bayes", "reader_count"=>62, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>8, "Researcher"=>19, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Student > Master"=>13, "Other"=>1, "Student > Bachelor"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>8, "Researcher"=>19, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Student > Master"=>13, "Other"=>1, "Student > Bachelor"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Mathematics"=>1, "Agricultural and Biological Sciences"=>44, "Computer Science"=>10, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>44}, "Computer Science"=>{"Computer Science"=>10}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"China"=>1, "Poland"=>1, "United Kingdom"=>2, "Australia"=>1, "France"=>2, "Switzerland"=>1, "Germany"=>2, "Spain"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/947349"], "description"=>"<p>The topology of the tree on the left gets modified into the tree on the right by swapping an aunt (A) and its niece (B). Nice–aunt swapping has been shown to be ergodic.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary biology", "genetics and genomics"], "article_id"=>617699, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Irmtraud M Meyer", "István Miklós"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0030149.g002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampling_of_Tree_Topologies_/617699", "title"=>"Sampling of Tree Topologies", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:10:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/947810"], "description"=>"<p>The name of each sequence indicates the NCBI accession number of the strain (see also <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0030149#pcbi-0030149-g006\" target=\"_blank\">Figure 6</a>)<b>.</b> The edge lengths in the left network correspond to the probability of the corresponding split in the posterior distribution, whereas the edge lengths in the right network correspond to the average length of the edge in the sampled trees.</p>", "links"=>[], "tags"=>["networks", "hdv", "dataset", "consisting", "15", "sequences"], "article_id"=>618148, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Irmtraud M Meyer", "István Miklós"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0030149.g008", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_Consensus_Networks_for_the_HDV_Dataset_Consisting_of_15_Sequences_of_HDV_Ribozymes_/618148", "title"=>"Two Consensus Networks for the HDV Dataset Consisting of 15 Sequences of HDV Ribozymes", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:14:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/947294"], "description"=>"<p>For calculating the gap contribution to the prior, <i>F</i><sub>3</sub>(<i>A</i>), we decompose the alignment into homogeneous groups based only on the pattern of the gaps in the alignment. Each asterisk represents a nucleotide in the alignment, and each dash denotes a gap in the alignment.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary biology", "genetics and genomics"], "article_id"=>617642, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Irmtraud M Meyer", "István Miklós"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0030149.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_Prior_/617642", "title"=>"Alignment Prior", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:09:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/947629"], "description"=>"<p>The name of each sequence indicates the NCBI accession number of the strain. The ribozyme contains one pseudoknot and a variable helix as shown in the line above the alignment, which denotes the known reference structure in dot-bracket, or Vienna, notation. The posterior probabilities for each alignment column were derived from the multiple sequence alignments that the MCMC method sampled and are indicated at the top of the figure.</p>", "links"=>[], "tags"=>["alignment", "hdv", "dataset", "consisting", "15", "sequences"], "article_id"=>617966, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Irmtraud M Meyer", "István Miklós"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0030149.g006", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MPD_Alignment_for_the_HDV_Dataset_Consisting_of_15_Sequences_of_HDV_Ribozymes_/617966", "title"=>"MPD Alignment for the HDV Dataset Consisting of 15 Sequences of HDV Ribozymes", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:13:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/947476"], "description"=>"<p>The pairing probabilities estimated by SimulFold are colour-coded and range from bright green (high probability) to bright red (low probability). The pairing probabilities for this structure range from 0.62 for the pair at sequence positions {4, 38} to one for most of the base-pairs, e.g., the one at sequence positions {6, 36}. For this figure, we have adopted a nonlinear colouring scheme; otherwise, all base-pairs would simply come in slightly different shades of green.</p>", "links"=>[], "tags"=>["pseudoknot", "simulfold", "hdv", "aj309880", "mcmc", "generated", "parallel"], "article_id"=>617807, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Irmtraud M Meyer", "István Miklós"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0030149.g004", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RNA_Structure_with_Pseudoknot_Predicted_by_SimulFold_for_the_HDV_Sequence_of_Organism_AJ309880_Using_the_MCMC_Results_Generated_with_Parallel_Tempering_/617807", "title"=>"RNA Structure with Pseudoknot Predicted by SimulFold for the HDV Sequence of Organism AJ309880 Using the MCMC Results Generated with Parallel Tempering", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:11:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/947528"], "description"=>"<p>With parallel tempering (grey) and without parallel tempering (black). Without parallel tempering, the MCMC chain gets stuck in local minima.</p>", "links"=>[], "tags"=>["steps", "mcmc", "hdv", "parallel"], "article_id"=>617877, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Irmtraud M Meyer", "István Miklós"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0030149.g005", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Loglikelihood_as_a_Function_of_the_Steps_in_the_MCMC_Chain_for_the_HDV_set_with_and_without_Parallel_Tempering_/617877", "title"=>"Loglikelihood as a Function of the Steps in the MCMC Chain for the HDV set with and without Parallel Tempering", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:13:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/947734"], "description"=>"<p>Some parts of the AB037948 and L22063 sequences are misaligned (red characters), which causes nonsense base-pairs (highlighted in green) when mapping the known reference structure onto these sequences.</p>", "links"=>[], "tags"=>["alignment", "hdv", "dataset", "consisting", "15", "sequences"], "article_id"=>618070, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Irmtraud M Meyer", "István Miklós"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0030149.g007", "stats"=>{"downloads"=>1, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustal_X_Alignment_for_the_HDV_Dataset_Consisting_of_15_Sequences_of_HDV_Ribozymes_/618070", "title"=>"Clustal-X Alignment for the HDV Dataset Consisting of 15 Sequences of HDV Ribozymes", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:14:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/947405"], "description"=>"<p>We sample a new alignment by choosing a random window of the alignment that is devoid of base-pairs and by realigning it (step 1). We then sample a new RNA structure by removing a random set of helices from the given structure (step 2) and by adding a set of new helices (step 3).</p>", "links"=>[], "tags"=>["alignment"], "article_id"=>617757, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Irmtraud M Meyer", "István Miklós"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0030149.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampling_Alignment_and_Structure_/617757", "title"=>"Sampling Alignment and Structure", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:10:40"}

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Relative Metric

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