IA Scholar Query: Counting All DCJ Sorting Scenarios.
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Internet Archive Scholar query results feedeninfo@archive.orgTue, 30 Aug 2022 00:00:00 GMTfatcat-scholarhttps://scholar.archive.org/help1440Sorting Genomes by Prefix Double-Cut-and-Joins
https://scholar.archive.org/work/7tuj5koizjah7g3y3eae3qnmxa
In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and recombine the severed endpoints in one of two possible ways: one of these options corresponds to a prefix reversal, which reverses the order of elements between the two cuts (as well as their signs in the signed case). Depending on whether we consider both options or reversals only, our main results are: (1) new structural lower bounds based on the breakpoint graph for sorting by unsigned prefix reversals, unsigned prefix DCJs, or signed prefix DCJs; (2) a polynomial-time algorithm for sorting by signed prefix DCJs, thus answering an open question in [8]; (3) a 3/2-approximation for sorting by unsigned prefix DCJs, which is, to the best of our knowledge, the first sorting by prefix rearrangements problem that admits an approximation ratio strictly smaller than 2 (with the obvious exception of the polynomial-time solvable problems); and finally, (4) an FPT algorithm for sorting by unsigned prefix DCJs parameterised by the number of breakpoints in the genome.Guillaume Fertin and Géraldine Jean and Anthony Labarrework_7tuj5koizjah7g3y3eae3qnmxaTue, 30 Aug 2022 00:00:00 GMTGene Orthology Inference via Large-Scale Rearrangements for Partially Assembled Genomes
https://scholar.archive.org/work/torlk3ub4nff7blq7szjge67pe
Recently we developed a gene orthology inference tool based on genome rearrangements (Journal of Bioinformatics and Computational Biology 19:6, 2021). Given a set of genomes our method first computes all pairwise gene similarities. Then it runs pairwise ILP comparisons to compute optimal gene matchings, which minimize, by taking the similarities into account, the weighted rearrangement distance between the analyzed genomes (a problem that is NP-hard). The gene matchings are then integrated into gene families in the final step. Although the ILP is quite efficient and could conceptually analyze genomes that are not completely assembled but split in several contigs, our tool failed in completing that task. The main reason is that each ILP pairwise comparison includes an optimal capping that connects each end of a linear segment of one genome to an end of a linear segment in the other genome, producing an exponential increase of the search space. In this work, we design and implement a heuristic capping algorithm that replaces the optimal capping by clustering (based on their gene content intersections) the linear segments into m ≥ 1 subsets, whose ends are capped independently. Furthermore, in each subset, instead of allowing all possible connections, we let only the ends of content-related segments be connected. Although there is no guarantee that m is much bigger than one, and with the possible side effect of resulting in sub-optimal instead of optimal gene matchings, the heuristic works very well in practice, from both the speed performance and the quality of computed solutions. Our experiments on real data show that we can now efficiently analyze fruit fly genomes with unfinished assemblies distributed in hundreds or even thousands of contigs, obtaining orthologies that are more similar to FlyBase orthologies when compared to orthologies computed by other inference tools. Moreover, for complete assemblies the version with heuristic capping reports orthologies that are very similar to the orthologies computed by [...]Diego P. Rubert, Marília D. V. Braga, Christina Boucher, Sven Rahmannwork_torlk3ub4nff7blq7szjge67peFri, 26 Aug 2022 00:00:00 GMTNew Algorithms for Structure Informed Genome Rearrangement
https://scholar.archive.org/work/jdrngh43fzedtf2hphpdxezzcu
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, Constrained TreeToString Divergence (CTTSD), we define the basic structure-informed rearrangement based divergence 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 the reference gene order. Then, a structure-informed gene rearrangement measure is computed between the ordered PQ-tree and the target gene order. The second problem, TreeToString Divergence (TTSD), generalizes CTTSD, where the gene order members are not necessarily permutations and the structure-informed rearrangement based divergence measure is extended to also consider up to d_S and d_T gene insertion and deletion operations, respectively, when modelling the PQ-tree informed divergence process from the reference order to the target order. The first algorithm solves CTTSD in O(n γ² ⋅ (m_p ⋅ 1.381^γ + m_q)) time and O(n²) space, where γ 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 m_p and m_q are the number of P-nodes and Q-nodes in the tree, respectively. If one of the penalties of CTTSD is 0, then the algorithm runs in O(n m γ²) time and O(n²) space. The second algorithm solves TTSD in O(n² γ² {d_T}² {d_S}² m² (m_p ⋅ 5^γ γ + m_q)) time and O(d_T d_S m (m n + 5^γ)) space, where γ 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, m_p and m_q are the number of P-nodes and Q-nodes in the tree, respectively, and allowing d_T deletions from the tree and d_S deletions from the st [...]Eden Ozery, Meirav Zehavi, Michal Ziv-Ukelson, Christina Boucher, Sven Rahmannwork_jdrngh43fzedtf2hphpdxezzcuFri, 26 Aug 2022 00:00:00 GMTEscape from Parsimony of Different Models of Genome Evolution Processes
https://scholar.archive.org/work/y6rq3tivszditjexr4xb7mvnu4
In the course of evolution, genomes diverge from their ancestors either via global mutations and by rearrangement of their chromosomal segments, or through local mutations within their genes. In this thesis (Chapters: 2, 3 and 4) we analyze the evolution of genomes based on different rearrangement operations including: in Chapter 2 both restricted and unrestricted double-cut-and-join (DCJ) operations, in Chapter 3 both internal and general reversal and translocation (IRT and HP, respectively) operations, and in Chapter 4 translocation, weighted reversal (WR) and maximum length reversal (MLR) operations. Based on the rearrangement operation chosen we can model the evolution of genomes as a discrete or continuous-time Markov chain process on the space of signed genomes. For each model of evolution, we study the stochastic process by investigating the time up to which the difference between the number of operations along the evolutionary trajectory and the edit distance of the genome from its ancestor is negligible, as soon as these two values starts diverging drastically from one another we say the process escapes from parsimony. One of the major parameters in the known edit distance formulas between any two genomes (such as reversal, DCJ, IRT, HP and translocation) is the number of cycles in their breakpoint graph. For DCJ, IRT and HP models by adopting the method elaborated by Berestycki and Durret, we estimate the number of cycles in the breakpoint graph of the genome at time t and its ancestor by the number of tree components of the random graph constructed from the model of evolution at time t, which is an Erdös-Rényi. We also proved that for each of the DCJ, IRT and HP models of evolution, the process on a genome of size n is bound to its parsimonious estimate up to t ≈ n/2 steps. Since the random graph constructed from the models of evolution for the translocation, WR and MLR processes are not Erdös-Rényi, the proofs of their parsimony- bound require more advanced mathematical tools, however our simulation s [...]Mona Meghdari Miardan, University, Mywork_y6rq3tivszditjexr4xb7mvnu4Wed, 09 Mar 2022 00:00:00 GMTUnderstanding for whom, how and why Sydney Local Health District's Integrated Response was Effective in Addressing COVID-19: A Critical Realist Qualitative Study
https://scholar.archive.org/work/32vtewddmzat3egryqdnaeswz4
Australia has been comparatively effective in preventing the transmission of COVID-19. The Sydney Local Health District [SLHD] used a "whole of health" integrated approach to respond to the pandemic. The aim of this study was to understand for whom, how and why this response worked, to inform a sustainable system transformation. A critical realist qualitative study was conducted with 20 purposively selected key informants. Data were collected through in-depth interviews and analysed using thematic analysis guided by abduction and retroduction. The five strategies of the WHO integrated people-centred health services framework was used to guide the overall study. An enabling environment of a strong governance, emergency preparedness, a committed and adaptable workforce, and a strong core infrastructure underpinned SLHD's effective response. With a culture of embracing innovation, the district adapted virtual care to effectively quarantine people through their special health accommodation, and coordinate care across tertiary and community services. The established interagency relationships prior to the pandemic, enabled service directors to quickly integrate their services, which empowered and engaged the community [and staff], working across relevant sectors to provide care "where the people are"; reaching marginalised populations, and reducing community transmission. The SLHD's progress towards a 'whole of health' approach, empowered and enabled the district to effectively work within and across sectors to address the pandemic in a people-centred manner. Sustaining the contextual conditions and mechanisms, that facilitated effective integration, will be beneficial beyond the pandemic.Hueiming Liu, Darith Liu, Corey Moore, Lisa Parcsi, Ferdinand Mukumbang, Denise De Souza, Miranda Shaw, Lou-Anne Blunden, Teresa Anderson, John Eastwoodwork_32vtewddmzat3egryqdnaeswz4Fri, 11 Feb 2022 00:00:00 GMTAgeing well in public housing
https://scholar.archive.org/work/2mrvak7ykjc2riyt2hr6fkbed4
This research examines the policy and practice issues raised by increasing demand for public housing among older Australians, and how public housing authorities can support older tenants to age well. People aged 55 years and over now comprise 35 per cent of public housing tenants nationally, in the coming years it is expected the demand on the public housing system from lower income older households will increase significantly.Debbie Faulkner, Julia Verdouw, Peta Cook, Selina Tually, Edgar Liu, Bruce Judd, Helen Barrie, Veronica Coramwork_2mrvak7ykjc2riyt2hr6fkbed4Thu, 11 Nov 2021 00:00:00 GMT