Algorithms for Molecular Biology最新文献

{"title":"Automated design of dynamic programming schemes for RNA folding with pseudoknots.","authors":"Bertrand Marchand, Sebastian Will, Sarah J Berkemer, Yann Ponty, Laurent Bulteau","doi":"10.1186/s13015-023-00229-z","DOIUrl":"10.1186/s13015-023-00229-z","url":null,"abstract":"<p><p>Although RNA secondary structure prediction is a textbook application of dynamic programming (DP) and routine task in RNA structure analysis, it remains challenging whenever pseudoknots come into play. Since the prediction of pseudoknotted structures by minimizing (realistically modelled) energy is NP-hard, specialized algorithms have been proposed for restricted conformation classes that capture the most frequently observed configurations. To achieve good performance, these methods rely on specific and carefully hand-crafted DP schemes. In contrast, we generalize and fully automatize the design of DP pseudoknot prediction algorithms. For this purpose, we formalize the problem of designing DP algorithms for an (infinite) class of conformations, modeled by (a finite number of) fatgraphs, and automatically build DP schemes minimizing their algorithmic complexity. We propose an algorithm for the problem, based on the tree-decomposition of a well-chosen representative structure, which we simplify and reinterpret as a DP scheme. The algorithm is fixed-parameter tractable for the treewidth tw of the fatgraph, and its output represents a [Formula: see text] algorithm (and even possibly [Formula: see text] in simple energy models) for predicting the MFE folding of an RNA of length n. We demonstrate, for the most common pseudoknot classes, that our automatically generated algorithms achieve the same complexities as reported in the literature for hand-crafted schemes. Our framework supports general energy models, partition function computations, recursive substructures and partial folding, and could pave the way for algebraic dynamic programming beyond the context-free case.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"18 1","pages":"18"},"PeriodicalIF":1.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10691146/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138471179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New algorithms for structure informed genome rearrangement.","authors":"Eden Ozeri, Meirav Zehavi, Michal Ziv-Ukelson","doi":"10.1186/s13015-023-00239-x","DOIUrl":"10.1186/s13015-023-00239-x","url":null,"abstract":"<p><p>We define two new computational problems in the domain of perfect genome rearrangements, and propose three algorithms to solve them. The rearrangement scenarios modeled by the problems consider Reversal and Block Interchange operations, and a PQ-tree is utilized to guide the allowed operations and to compute their weights. In the first problem, [Formula: see text] ([Formula: see text]), we define the basic structure-informed rearrangement measure. Here, we assume that the gene order members of the gene cluster from which the PQ-tree is constructed are permutations. The PQ-tree representing the gene cluster is ordered such that the series of gene IDs spelled by its leaves is equivalent to that of the reference gene order. Then, a structure-informed genome rearrangement distance is computed between the ordered PQ-tree and the target gene order. The second problem, [Formula: see text] ([Formula: see text]), generalizes [Formula: see text], where the gene order members are not necessarily permutations and the structure informed rearrangement measure is extended to also consider up to [Formula: see text] and [Formula: see text] gene insertion and deletion operations, respectively, when modelling the PQ-tree informed divergence process from the reference gene order to the target gene order. The first algorithm solves [Formula: see text] in [Formula: see text] time and [Formula: see text] space, where [Formula: see text] is the maximum number of children of a node, n is the length of the string and the number of leaves in the tree, and [Formula: see text] and [Formula: see text] are the number of P-nodes and Q-nodes in the tree, respectively. If one of the penalties of [Formula: see text] is 0, then the algorithm runs in [Formula: see text] time and [Formula: see text] space. The second algorithm solves [Formula: see text] in [Formula: see text] time and [Formula: see text] space, where [Formula: see text] is the maximum number of children of a node, n is the length of the string, m is the number of leaves in the tree, [Formula: see text] and [Formula: see text] are the number of P-nodes and Q-nodes in the tree, respectively, and allowing up to [Formula: see text] deletions from the tree and up to [Formula: see text] deletions from the string. The third algorithm is intended to reduce the space complexity of the second algorithm. It solves a variant of the problem (where one of the penalties of [Formula: see text] is 0) in [Formula: see text] time and [Formula: see text] space. The algorithm is implemented as a software tool, denoted MEM-Rearrange, and applied to the comparative and evolutionary analysis of 59 chromosomal gene clusters extracted from a dataset of 1487 prokaryotic genomes.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"18 1","pages":"17"},"PeriodicalIF":1.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10691145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138464177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Relative timing information and orthology in evolutionary scenarios.","authors":"David Schaller, Tom Hartmann, Manuel Lafond, Peter F Stadler, Nicolas Wieseke, Marc Hellmuth","doi":"10.1186/s13015-023-00240-4","DOIUrl":"10.1186/s13015-023-00240-4","url":null,"abstract":"<p><strong>Background: </strong>Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves of S) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event. The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph.</p><p><strong>Results: </strong>Here we give a complete characterization in terms of informative and forbidden triples that can be read off the three graphs and provide a polynomial time algorithm for constructing an evolutionary scenario that explains the graphs, provided such a scenario exists. While both LDT and PDT graphs are cographs, this is not true for the EDT graph in general. We show that every EDT graph is perfect. While the information about LDT and PDT graphs is necessary to recognize EDT graphs in polynomial-time for general scenarios, this extra information can be dropped in the HGT-free case. However, recognition of EDT graphs without knowledge of putative LDT and PDT graphs is NP-complete for general scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We finally connect the EDT graph to the alternative definitions of orthology that have been proposed for scenarios with horizontal gene transfer. With one exception, the corresponding graphs are shown to be colored cographs.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"18 1","pages":"16"},"PeriodicalIF":1.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71523304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Embedding gene trees into phylogenetic networks by conflict resolution algorithms","authors":"Marcin Wawerka, D. Dabkowski, Natalia Rutecka, Agnieszka Mykowiecka, P. Górecki","doi":"10.1186/s13015-022-00218-8","DOIUrl":"https://doi.org/10.1186/s13015-022-00218-8","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"76 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78686342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bi-alignments with affine gaps costs","authors":"Peter F. Stadler, S. Will","doi":"10.1186/s13015-022-00219-7","DOIUrl":"https://doi.org/10.1186/s13015-022-00219-7","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"1 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2022-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82802988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adding hydrogen atoms to molecular models via fragment superimposition","authors":"Patrick Kunzmann, Jacob Marcel Anter, K. Hamacher","doi":"10.1186/s13015-022-00215-x","DOIUrl":"https://doi.org/10.1186/s13015-022-00215-x","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2022-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65741668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parsimonious Clone Tree Integration in cancer","authors":"P. Sashittal, Simone Zaccaria, M. El-Kebir","doi":"10.1186/s13015-022-00209-9","DOIUrl":"https://doi.org/10.1186/s13015-022-00209-9","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2022-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86681252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics","authors":"Bertrand Marchand, Y. Ponty, L. Bulteau","doi":"10.1186/s13015-022-00213-z","DOIUrl":"https://doi.org/10.1186/s13015-022-00213-z","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2021-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65742120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics.","authors":"Christophe Ambroise,&nbsp;Alia Dehman,&nbsp;Pierre Neuvial,&nbsp;Guillem Rigaill,&nbsp;Nathalie Vialaneix","doi":"10.1186/s13015-019-0157-4","DOIUrl":"https://doi.org/10.1186/s13015-019-0157-4","url":null,"abstract":"<p><strong>Background: </strong>Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-resolution, locus-level measurements. An intuitive way of doing this is to perform a modified Hierarchical Agglomerative Clustering (HAC), where only adjacent clusters (according to the ordering of positions within a chromosome) are allowed to be merged. But a major practical drawback of this method is its quadratic time and space complexity in the number of loci, which is typically of the order of <math><msup><mn>10</mn> <mn>4</mn></msup> </math> to <math><msup><mn>10</mn> <mn>5</mn></msup> </math> for each chromosome.</p><p><strong>Results: </strong>By assuming that the similarity between physically distant objects is negligible, we are able to propose an implementation of adjacency-constrained HAC with quasi-linear complexity. This is achieved by pre-calculating specific sums of similarities, and storing candidate fusions in a min-heap. Our illustrations on GWAS and Hi-C datasets demonstrate the relevance of this assumption, and show that this method highlights biologically meaningful signals. Thanks to its small time and memory footprint, the method can be run on a standard laptop in minutes or even seconds.</p><p><strong>Availability and implementation: </strong>Software and sample data are available as an R package, <b>adjclust</b>, that can be downloaded from the Comprehensive R Archive Network (CRAN).</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"14 ","pages":"22"},"PeriodicalIF":1.0,"publicationDate":"2019-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-019-0157-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49684571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using a constraint-based regression method for relative quantification of somatic mutations in pyrosequencing signals: a case for NRAS analysis","authors":"J. Ambroise, Jamal Badir, Louise Nienhaus, Annie Robert, A. Dekairelle, J. Gala","doi":"10.1186/s13015-016-0086-4","DOIUrl":"https://doi.org/10.1186/s13015-016-0086-4","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"11 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2016-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-016-0086-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65742106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}