Algorithms for Molecular Biology最新文献

{"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":"Improving metagenomic binning results with overlapped bins using assembly graphs.","authors":"Vijini G Mallawaarachchi,&nbsp;Anuradha S Wickramarachchi,&nbsp;Yu Lin","doi":"10.1186/s13015-021-00185-6","DOIUrl":"https://doi.org/10.1186/s13015-021-00185-6","url":null,"abstract":"<p><strong>Background: </strong>Metagenomic sequencing allows us to study the structure, diversity and ecology in microbial communities without the necessity of obtaining pure cultures. In many metagenomics studies, the reads obtained from metagenomics sequencing are first assembled into longer contigs and these contigs are then binned into clusters of contigs where contigs in a cluster are expected to come from the same species. As different species may share common sequences in their genomes, one assembled contig may belong to multiple species. However, existing tools for binning contigs only support non-overlapped binning, i.e., each contig is assigned to at most one bin (species).</p><p><strong>Results: </strong>In this paper, we introduce GraphBin2 which refines the binning results obtained from existing tools and, more importantly, is able to assign contigs to multiple bins. GraphBin2 uses the connectivity and coverage information from assembly graphs to adjust existing binning results on contigs and to infer contigs shared by multiple species. Experimental results on both simulated and real datasets demonstrate that GraphBin2 not only improves binning results of existing tools but also supports to assign contigs to multiple bins.</p><p><strong>Conclusion: </strong>GraphBin2 incorporates the coverage information into the assembly graph to refine the binning results obtained from existing binning tools. GraphBin2 also enables the detection of contigs that may belong to multiple species. We show that GraphBin2 outperforms its predecessor GraphBin on both simulated and real datasets. GraphBin2 is freely available at https://github.com/Vini2/GraphBin2 .</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"16 1","pages":"3"},"PeriodicalIF":1.0,"publicationDate":"2021-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-021-00185-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38869054","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":"Fast lightweight accurate xenograft sorting.","authors":"Jens Zentgraf,&nbsp;Sven Rahmann","doi":"10.1186/s13015-021-00181-w","DOIUrl":"https://doi.org/10.1186/s13015-021-00181-w","url":null,"abstract":"<p><strong>Motivation: </strong>With an increasing number of patient-derived xenograft (PDX) models being created and subsequently sequenced to study tumor heterogeneity and to guide therapy decisions, there is a similarly increasing need for methods to separate reads originating from the graft (human) tumor and reads originating from the host species' (mouse) surrounding tissue. Two kinds of methods are in use: On the one hand, alignment-based tools require that reads are mapped and aligned (by an external mapper/aligner) to the host and graft genomes separately first; the tool itself then processes the resulting alignments and quality metrics (typically BAM files) to assign each read or read pair. On the other hand, alignment-free tools work directly on the raw read data (typically FASTQ files). Recent studies compare different approaches and tools, with varying results.</p><p><strong>Results: </strong>We show that alignment-free methods for xenograft sorting are superior concerning CPU time usage and equivalent in accuracy. We improve upon the state of the art sorting by presenting a fast lightweight approach based on three-way bucketed quotiented Cuckoo hashing. Our hash table requires memory comparable to an FM index typically used for read alignment and less than other alignment-free approaches. It allows extremely fast lookups and uses less CPU time than other alignment-free methods and alignment-based methods at similar accuracy. Several engineering steps (e.g., shortcuts for unsuccessful lookups, software prefetching) improve the performance even further.</p><p><strong>Availability: </strong>Our software xengsort is available under the MIT license at http://gitlab.com/genomeinformatics/xengsort . It is written in numba-compiled Python and comes with sample Snakemake workflows for hash table construction and dataset processing.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"16 1","pages":"2"},"PeriodicalIF":1.0,"publicationDate":"2021-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-021-00181-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25554318","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":"Quantifying steric hindrance and topological obstruction to protein structure superposition.","authors":"Peter Røgen","doi":"10.1186/s13015-020-00180-3","DOIUrl":"https://doi.org/10.1186/s13015-020-00180-3","url":null,"abstract":"<p><strong>Background: </strong>In computational structural biology, structure comparison is fundamental for our understanding of proteins. Structure comparison is, e.g., algorithmically the starting point for computational studies of structural evolution and it guides our efforts to predict protein structures from their amino acid sequences. Most methods for structural alignment of protein structures optimize the distances between aligned and superimposed residue pairs, i.e., the distances traveled by the aligned and superimposed residues during linear interpolation. Considering such a linear interpolation, these methods do not differentiate if there is room for the interpolation, if it causes steric clashes, or more severely, if it changes the topology of the compared protein backbone curves.</p><p><strong>Results: </strong>To distinguish such cases, we analyze the linear interpolation between two aligned and superimposed backbones. We quantify the amount of steric clashes and find all self-intersections in a linear backbone interpolation. To determine if the self-intersections alter the protein's backbone curve significantly or not, we present a path-finding algorithm that checks if there exists a self-avoiding path in a neighborhood of the linear interpolation. A new path is constructed by altering the linear interpolation using a novel interpretation of Reidemeister moves from knot theory working on three-dimensional curves rather than on knot diagrams. Either the algorithm finds a self-avoiding path or it returns a smallest set of essential self-intersections. Each of these indicates a significant difference between the folds of the aligned protein structures. As expected, we find at least one essential self-intersection separating most unknotted structures from a knotted structure, and we find even larger motions in proteins connected by obstruction free linear interpolations. We also find examples of homologous proteins that are differently threaded, and we find many distinct folds connected by longer but simple deformations. TM-align is one of the most restrictive alignment programs. With standard parameters, it only aligns residues superimposed within 5 Ångström distance. We find 42165 topological obstructions between aligned parts in 142068 TM-alignments. Thus, this restrictive alignment procedure still allows topological dissimilarity of the aligned parts.</p><p><strong>Conclusions: </strong>Based on the data we conclude that our program ProteinAlignmentObstruction provides significant additional information to alignment scores based solely on distances between aligned and superimposed residue pairs.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"16 1","pages":"1"},"PeriodicalIF":1.0,"publicationDate":"2021-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-020-00180-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25411733","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":"gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections.","authors":"Felipe A Louza,&nbsp;Guilherme P Telles,&nbsp;Simon Gog,&nbsp;Nicola Prezza,&nbsp;Giovanna Rosone","doi":"10.1186/s13015-020-00177-y","DOIUrl":"https://doi.org/10.1186/s13015-020-00177-y","url":null,"abstract":"<p><strong>Background: </strong>The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings. Related data structures, as the Longest Common Prefix array, the Burrows-Wheeler transform, and the document array, are often needed to accompany the suffix array to efficiently solve a wide variety of problems. While several algorithms have been proposed to construct the suffix array for a single string, less emphasis has been put on algorithms to construct suffix arrays for string collections.</p><p><strong>Result: </strong>In this paper we introduce gsufsort, an open source software for constructing the suffix array and related data indexing structures for a string collection with <i>N</i> symbols in <i>O</i>(<i>N</i>) time. Our tool is written in ANSI/C and is based on the algorithm gSACA-K (Louza et al. in Theor Comput Sci 678:22-39, 2017), the fastest algorithm to construct suffix arrays for string collections. The tool supports large fasta, fastq and text files with multiple strings as input. Experiments have shown very good performance on different types of strings.</p><p><strong>Conclusions: </strong>gsufsort is a fast, portable, and lightweight tool for constructing the suffix array and additional data structures for string collections.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"15 ","pages":"18"},"PeriodicalIF":1.0,"publicationDate":"2020-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-020-00177-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38417629","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":"A linear-time algorithm that avoids inverses and computes Jackknife (leave-one-out) products like convolutions or other operators in commutative semigroups.","authors":"John L Spouge,&nbsp;Joseph M Ziegelbauer,&nbsp;Mileidy Gonzalez","doi":"10.1186/s13015-020-00178-x","DOIUrl":"https://doi.org/10.1186/s13015-020-00178-x","url":null,"abstract":"<p><strong>Background: </strong>Data about herpesvirus microRNA motifs on human circular RNAs suggested the following statistical question. Consider independent random counts, not necessarily identically distributed. Conditioned on the sum, decide whether one of the counts is unusually large. Exact computation of the p<i>-</i>value leads to a specific algorithmic problem. Given <math><mi>n</mi></math> elements <math> <mrow><msub><mi>g</mi> <mn>0</mn></msub> <mo>,</mo> <msub><mi>g</mi> <mn>1</mn></msub> <mo>,</mo> <mo>…</mo> <mo>,</mo> <msub><mi>g</mi> <mrow><mi>n</mi> <mo>-</mo> <mn>1</mn></mrow> </msub> </mrow> </math> in a set <math><mi>G</mi></math> with the closure and associative properties and a commutative product without inverses, compute the jackknife (leave-one-out) products <math> <mrow> <msub> <mover><mrow><mi>g</mi></mrow> <mrow><mo>¯</mo></mrow> </mover> <mi>j</mi></msub> <mo>=</mo> <msub><mi>g</mi> <mn>0</mn></msub> <msub><mi>g</mi> <mn>1</mn></msub> <mo>⋯</mo> <msub><mi>g</mi> <mrow><mi>j</mi> <mo>-</mo> <mn>1</mn></mrow> </msub> <msub><mi>g</mi> <mrow><mi>j</mi> <mo>+</mo> <mn>1</mn></mrow> </msub> <mo>⋯</mo> <msub><mi>g</mi> <mrow><mi>n</mi> <mo>-</mo> <mn>1</mn></mrow> </msub> </mrow> </math> ( <math><mrow><mn>0</mn> <mo>≤</mo> <mi>j</mi> <mo><</mo> <mi>n</mi></mrow> </math> ).</p><p><strong>Results: </strong>This article gives a linear-time Jackknife Product algorithm. Its upward phase constructs a standard segment tree for computing segment products like <math> <mrow><msub><mi>g</mi> <mfenced><mrow><mi>i</mi> <mo>,</mo> <mi>j</mi></mrow> </mfenced> </msub> <mo>=</mo> <msub><mi>g</mi> <mi>i</mi></msub> <msub><mi>g</mi> <mrow><mi>i</mi> <mo>+</mo> <mn>1</mn></mrow> </msub> <mo>⋯</mo> <msub><mi>g</mi> <mrow><mi>j</mi> <mo>-</mo> <mn>1</mn></mrow> </msub> </mrow> </math> ; its novel downward phase mirrors the upward phase while exploiting the symmetry of <math><msub><mi>g</mi> <mi>j</mi></msub> </math> and its complement <math> <msub> <mover><mrow><mi>g</mi></mrow> <mrow><mo>¯</mo></mrow> </mover> <mi>j</mi></msub> </math> . The algorithm requires storage for <math><mrow><mn>2</mn> <mi>n</mi></mrow> </math> elements of <math><mi>G</mi></math> and only about <math><mrow><mn>3</mn> <mi>n</mi></mrow> </math> products. In contrast, the standard segment tree algorithms require about <math><mi>n</mi></math> products for construction and <math> <mrow><msub><mo>log</mo> <mn>2</mn></msub> <mi>n</mi></mrow> </math> products for calculating each <math> <msub> <mover><mrow><mi>g</mi></mrow> <mrow><mo>¯</mo></mrow> </mover> <mi>j</mi></msub> </math> , i.e., about <math><mrow><mi>n</mi> <msub><mo>log</mo> <mn>2</mn></msub> <mi>n</mi></mrow> </math> products in total; and a naïve quadratic algorithm using <math><mrow><mi>n</mi> <mo>-</mo> <mn>2</mn></mrow> </math> element-by-element products to compute each <math> <msub> <mover><mrow><mi>g</mi></mrow> <mrow><mo>¯</mo></mrow> </mover> <mi>j</mi></msub> </math> requires <math><mrow><mi>n</mi> <mf","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"15 ","pages":"17"},"PeriodicalIF":1.0,"publicationDate":"2020-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-020-00178-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38415649","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":"On an enhancement of RNA probing data using information theory.","authors":"Thomas J X Li,&nbsp;Christian M Reidys","doi":"10.1186/s13015-020-00176-z","DOIUrl":"https://doi.org/10.1186/s13015-020-00176-z","url":null,"abstract":"<p><p>Identifying the secondary structure of an RNA is crucial for understanding its diverse regulatory functions. This paper focuses on how to enhance target identification in a Boltzmann ensemble of structures via chemical probing data. We employ an information-theoretic approach to solve the problem, via considering a variant of the Rényi-Ulam game. Our framework is centered around the ensemble tree, a hierarchical bi-partition of the input ensemble, that is constructed by recursively querying about whether or not a base pair of maximum information entropy is contained in the target. These queries are answered via relating local with global probing data, employing the modularity in RNA secondary structures. We present that leaves of the tree are comprised of sub-samples exhibiting a distinguished structure with high probability. In particular, for a Boltzmann ensemble incorporating probing data, which is well established in the literature, the probability of our framework correctly identifying the target in the leaf is greater than <math><mrow><mn>90</mn> <mo>%</mo></mrow> </math> .</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"15 ","pages":"15"},"PeriodicalIF":1.0,"publicationDate":"2020-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-020-00176-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38252398","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":"Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility.","authors":"Tiziana Calamoneri,&nbsp;Mattia Gastaldello,&nbsp;Arnaud Mary,&nbsp;Marie-France Sagot,&nbsp;Blerina Sinaimeri","doi":"10.1186/s13015-020-00174-1","DOIUrl":"https://doi.org/10.1186/s13015-020-00174-1","url":null,"abstract":"<p><p>Cytoplasmic incompatibility (CI) relates to the manipulation by the parasite <i>Wolbachia</i> of its host reproduction. Despite its widespread occurrence, the molecular basis of CI remains unclear and theoretical models have been proposed to understand the phenomenon. We consider in this paper the quantitative Lock-Key model which currently represents a good hypothesis that is consistent with the data available. CI is in this case modelled as the problem of covering the edges of a bipartite graph with the minimum number of chain subgraphs. This problem is already known to be NP-hard, and we provide an exponential algorithm with a non trivial complexity. It is frequent that depending on the dataset, there may be many optimal solutions which can be biologically quite different among them. To rely on a single optimal solution may therefore be problematic. To this purpose, we address the problem of enumerating (listing) all minimal chain subgraph covers of a bipartite graph and show that it can be solved in quasi-polynomial time. Interestingly, in order to solve the above problems, we considered also the problem of enumerating all the maximal chain subgraphs of a bipartite graph and improved on the current results in the literature for the latter. Finally, to demonstrate the usefulness of our methods we show an application on a real dataset.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"15 ","pages":"14"},"PeriodicalIF":1.0,"publicationDate":"2020-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-020-00174-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38186822","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":"Fast computation of genome-metagenome interaction effects.","authors":"Florent Guinot,&nbsp;Marie Szafranski,&nbsp;Julien Chiquet,&nbsp;Anouk Zancarini,&nbsp;Christine Le Signor,&nbsp;Christophe Mougel,&nbsp;Christophe Ambroise","doi":"10.1186/s13015-020-00173-2","DOIUrl":"https://doi.org/10.1186/s13015-020-00173-2","url":null,"abstract":"<p><strong>Motivation: </strong>Association studies have been widely used to search for associations between common genetic variants observations and a given phenotype. However, it is now generally accepted that genes and environment must be examined jointly when estimating phenotypic variance. In this work we consider two types of biological markers: genotypic markers, which characterize an observation in terms of inherited genetic information, and metagenomic marker which are related to the environment. Both types of markers are available in their millions and can be used to characterize any observation uniquely.</p><p><strong>Objective: </strong>Our focus is on detecting interactions between groups of genetic and metagenomic markers in order to gain a better understanding of the complex relationship between environment and genome in the expression of a given phenotype.</p><p><strong>Contributions: </strong>We propose a novel approach for efficiently detecting interactions between complementary datasets in a high-dimensional setting with a reduced computational cost. The method, named SICOMORE, reduces the dimension of the search space by selecting a subset of supervariables in the two complementary datasets. These supervariables are given by a weighted group structure defined on sets of variables at different scales. A Lasso selection is then applied on each type of supervariable to obtain a subset of potential interactions that will be explored via linear model testing.</p><p><strong>Results: </strong>We compare SICOMORE with other approaches in simulations, with varying sample sizes, noise, and numbers of true interactions. SICOMORE exhibits convincing results in terms of recall, as well as competitive performances with respect to running time. The method is also used to detect interaction between genomic markers in <i>Medicago truncatula</i> and metagenomic markers in its rhizosphere bacterial community.</p><p><strong>Software availability: </strong>An R package is available [4], along with its documentation and associated scripts, allowing the reader to reproduce the results presented in the paper.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"15 ","pages":"13"},"PeriodicalIF":1.0,"publicationDate":"2020-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-020-00173-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38119459","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":"Evolution through segmental duplications and losses: a Super-Reconciliation approach.","authors":"Mattéo Delabre,&nbsp;Nadia El-Mabrouk,&nbsp;Katharina T Huber,&nbsp;Manuel Lafond,&nbsp;Vincent Moulton,&nbsp;Emmanuel Noutahi,&nbsp;Miguel Sautie Castellanos","doi":"10.1186/s13015-020-00171-4","DOIUrl":"https://doi.org/10.1186/s13015-020-00171-4","url":null,"abstract":"<p><p>The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is not appropriate for genes grouped into syntenic blocks, which are more plausibly the result of a concerted evolution. Here, we introduce the <i>Super-Reconciliation</i> problem which consists in inferring a history of segmental duplication and loss events (involving a set of neighboring genes) leading to a set of present-day syntenies from a single ancestral one. In other words, we extend the traditional Duplication-Loss reconciliation problem of a single gene tree, to a set of trees, accounting for segmental duplications and losses. Existency of a Super-Reconciliation depends on individual gene tree consistency. In addition, ignoring rearrangements implies that existency also depends on gene order consistency. We first show that the problem of reconstructing a most parsimonious Super-Reconciliation, if any, is NP-hard and give an exact exponential-time algorithm to solve it. Alternatively, we show that accounting for rearrangements in the evolutionary model, but still only minimizing segmental duplication and loss events, leads to an exact polynomial-time algorithm. We finally assess time efficiency of the former exponential time algorithm for the Duplication-Loss model on simulated datasets, and give a proof of concept on the opioid receptor genes.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"15 ","pages":"12"},"PeriodicalIF":1.0,"publicationDate":"2020-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-020-00171-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38022547","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}