Algorithms for Molecular Biology最新文献

{"title":"Co-linear chaining on pangenome graphs.","authors":"Jyotshna Rajput, Ghanshyam Chandra, Chirag Jain","doi":"10.1186/s13015-024-00250-w","DOIUrl":"10.1186/s13015-024-00250-w","url":null,"abstract":"<p><p>Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to these graphs with complex topology and cycles can be challenging. The seed-chain-extend based alignment algorithms use co-linear chaining as a standard technique to identify a good cluster of exact seed matches that can be combined to form an alignment. Recent works show how the co-linear chaining problem can be efficiently solved for acyclic pangenome graphs by exploiting their small width and how incorporating gap cost in the scoring function improves alignment accuracy. However, it remains open on how to effectively generalize these techniques for general pangenome graphs which contain cycles. Here we present the first practical formulation and an exact algorithm for co-linear chaining on cyclic pangenome graphs. We rigorously prove the correctness and computational complexity of the proposed algorithm. We evaluate the empirical performance of our algorithm by aligning simulated long reads from the human genome to a cyclic pangenome graph constructed from 95 publicly available haplotype-resolved human genome assemblies. While the existing heuristic-based algorithms are faster, the proposed algorithm provides a significant advantage in terms of accuracy. Implementation ( https://github.com/at-cg/PanAligner ).</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"19 1","pages":"4"},"PeriodicalIF":1.5,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11288099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139567423","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":"Fulgor: a fast and compact k-mer index for large-scale matching and color queries.","authors":"Jason Fan, Jamshed Khan, Noor Pratap Singh, Giulio Ermanno Pibiri, Rob Patro","doi":"10.1186/s13015-024-00251-9","DOIUrl":"10.1186/s13015-024-00251-9","url":null,"abstract":"<p><p>The problem of sequence identification or matching-determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence-is relevant for many important tasks in Computational Biology, such as metagenomics and pangenome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resource-efficient solution to this problem is of utmost importance. This poses the threefold challenge of representing the reference collection with a data structure that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe an efficient colored de Bruijn graph index, arising as the combination of a k-mer dictionary with a compressed inverted index. The proposed index takes full advantage of the fact that unitigs in the colored compacted de Bruijn graph are monochromatic (i.e., all k-mers in a unitig have the same set of references of origin, or color). Specifically, the unitigs are kept in the dictionary in color order, thereby allowing for the encoding of the map from k-mers to their colors in as little as 1 + o(1) bits per unitig. Hence, one color per unitig is stored in the index with almost no space/time overhead. By combining this property with simple but effective compression methods for integer lists, the index achieves very small space. We implement these methods in a tool called Fulgor, and conduct an extensive experimental analysis to demonstrate the improvement of our tool over previous solutions. For example, compared to Themisto-the strongest competitor in terms of index space vs. query time trade-off-Fulgor requires significantly less space (up to 43% less space for a collection of 150,000 Salmonella enterica genomes), is at least twice as fast for color queries, and is 2-6[Formula: see text] faster to construct.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"19 1","pages":"3"},"PeriodicalIF":1.5,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10810250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139522095","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":"Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem.","authors":"Junyan Dai, Tobias Rubel, Yunheng Han, Erin K Molloy","doi":"10.1186/s13015-023-00249-9","DOIUrl":"10.1186/s13015-023-00249-9","url":null,"abstract":"<p><p>The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal with respect to some objective function and that lies within a constrained version of tree space. The popular species tree estimation method ASTRAL, for example, returns a tree that (1) maximizes the quartet score computed with respect to the input gene trees and that (2) draws its branches (bipartitions) from the input constraint set. This technique has yet to be used for parsimony problems where the input are binary characters, sometimes with missing values. Here, we introduce the clade-constrained character parsimony problem and present an algorithm that solves this problem for the Dollo criterion score in [Formula: see text] time, where n is the number of leaves, k is the number of characters, and [Formula: see text] is the set of clades used as constraints. Dollo parsimony, which requires traits/mutations to be gained at most once but allows them to be lost any number of times, is widely used for tumor phylogenetics as well as species phylogenetics, for example analyses of low-homoplasy retroelement insertions across the vertebrate tree of life. This motivated us to implement our algorithm in a software package, called Dollo-CDP, and evaluate its utility for analyzing retroelement insertion presence / absence patterns for bats, birds, toothed whales as well as simulated data. Our results show that Dollo-CDP can improve upon heuristic search from a single starting tree, often recovering a better scoring tree. Moreover, Dollo-CDP scales to data sets with much larger numbers of taxa than branch-and-bound while still having an optimality guarantee, albeit a more restricted one. Lastly, we show that our algorithm for Dollo parsimony can easily be adapted to Camin-Sokal parsimony but not Fitch parsimony.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"19 1","pages":"2"},"PeriodicalIF":1.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10775561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139405043","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":"Investigating the complexity of the double distance problems","authors":"Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye","doi":"10.1186/s13015-023-00246-y","DOIUrl":"https://doi.org/10.1186/s13015-023-00246-y","url":null,"abstract":"Two genomes $$mathbb {A}$$ and $$mathbb {B}$$ over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Denote by $$n_*$$ the number of common families of $$mathbb {A}$$ and $$mathbb {B}$$ . Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents the relation between the two given genomes as a collection of cycles of even length and paths. Let $$c_i$$ and $$p_j$$ be respectively the numbers of cycles of length i and of paths of length j in the breakpoint graph of genomes $$mathbb {A}$$ and $$mathbb {B}$$ . Then, the breakpoint distance of $$mathbb {A}$$ and $$mathbb {B}$$ is equal to $$n_*-left( c_2+frac{p_0}{2}right)$$ . Similarly, when the considered rearrangements are those modeled by the double-cut-and-join (DCJ) operation, the rearrangement distance of $$mathbb {A}$$ and $$mathbb {B}$$ is $$n_*-left( c+frac{p_e }{2}right)$$ , where c is the total number of cycles and $$p_e$$ is the total number of paths of even length. The distance formulation is a basic unit for several other combinatorial problems related to genome evolution and ancestral reconstruction, such as median or double distance. Interestingly, both median and double distance problems can be solved in polynomial time for the breakpoint distance, while they are NP-hard for the rearrangement distance. One way of exploring the complexity space between these two extremes is to consider a $$sigma _k$$ distance, defined to be $$n_*-left( c_2+c_4+ldots +c_k+frac{p_0+p_2+ldots +p_{k-2}}{2}right)$$ , and increasingly investigate the complexities of median and double distance for the $$sigma _4$$ distance, then the $$sigma _6$$ distance, and so on. While for the median much effort was done in our and in other research groups but no progress was obtained even for the $$sigma _4$$ distance, for solving the double distance under $$sigma _4$$ and $$sigma _6$$ distances we could devise linear time algorithms, which we present here.","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"19 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139095860","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":"EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment","authors":"Chengze Shen, Baqiao Liu, Kelly P. Williams, Tandy Warnow","doi":"10.1186/s13015-023-00247-x","DOIUrl":"https://doi.org/10.1186/s13015-023-00247-x","url":null,"abstract":"Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledge, or computing alignments in the presence of sequence length heterogeneity. Although this is a natural problem, only a few tools have been developed to use this information with high fidelity. We present EMMA (Extending Multiple alignments using MAFFT--add) for the problem of adding a set of unaligned sequences into a multiple sequence alignment (i.e., a constraint alignment). EMMA builds on MAFFT--add, which is also designed to add sequences into a given constraint alignment. EMMA improves on MAFFT--add methods by using a divide-and-conquer framework to scale its most accurate version, MAFFT-linsi--add, to constraint alignments with many sequences. We show that EMMA has an accuracy advantage over other techniques for adding sequences into alignments under many realistic conditions and can scale to large datasets with high accuracy (hundreds of thousands of sequences). EMMA is available at https://github.com/c5shen/EMMA . EMMA is a new tool that provides high accuracy and scalability for adding sequences into an existing alignment.","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"23 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138555235","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":"Correction: Constructing founder sets under allelic and non-allelic homologous recombination.","authors":"Konstantinn Bonnet, Tobias Marschall, Daniel Doerr","doi":"10.1186/s13015-023-00244-0","DOIUrl":"10.1186/s13015-023-00244-0","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"18 1","pages":"20"},"PeriodicalIF":1.0,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10698948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138500077","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":"Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model.","authors":"Yunheng Han, Erin K Molloy","doi":"10.1186/s13015-023-00248-w","DOIUrl":"10.1186/s13015-023-00248-w","url":null,"abstract":"<p><p>Cancer progression and treatment can be informed by reconstructing its evolutionary history from tumor cells. Although many methods exist to estimate evolutionary trees (called phylogenies) from molecular sequences, traditional approaches assume the input data are error-free and the output tree is fully resolved. These assumptions are challenged in tumor phylogenetics because single-cell sequencing produces sparse, error-ridden data and because tumors evolve clonally. Here, we study the theoretical utility of methods based on quartets (four-leaf, unrooted phylogenetic trees) in light of these barriers. We consider a popular tumor phylogenetics model, in which mutations arise on a (highly unresolved) tree and then (unbiased) errors and missing values are introduced. Quartets are then implied by mutations present in two cells and absent from two cells. Our main result is that the most probable quartet identifies the unrooted model tree on four cells. This motivates seeking a tree such that the number of quartets shared between it and the input mutations is maximized. We prove an optimal solution to this problem is a consistent estimator of the unrooted cell lineage tree; this guarantee includes the case where the model tree is highly unresolved, with error defined as the number of false negative branches. Lastly, we outline how quartet-based methods might be employed when there are copy number aberrations and other challenges specific to tumor phylogenetics.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"18 1","pages":"19"},"PeriodicalIF":1.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10691101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138471180","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":"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}