scholarly journals Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i668-i674
Author(s):  
Huy N Nguyen ◽  
Alexey Markin ◽  
Iddo Friedberg ◽  
Oliver Eulenstein
Keyword(s):  
Complex Traits ◽  
Heuristic Method ◽  
Orthologous Gene ◽  
Homologous Gene ◽  
Modern Biology ◽  
Program Problem ◽  
Gene Block ◽  
Linear Program Problem ◽  
Small Set ◽  
Vertical Evolution

Abstract Motivation The evolution of complexity is one of the most fascinating and challenging problems in modern biology, and tracing the evolution of complex traits is an open problem. In bacteria, operons and gene blocks provide a model of tractable evolutionary complexity at the genomic level. Gene blocks are structures of co-located genes with related functions, and operons are gene blocks whose genes are co-transcribed on a single mRNA molecule. The genes in operons and gene blocks typically work together in the same system or molecular complex. Previously, we proposed a method that explains the evolution of orthologous gene blocks (orthoblocks) as a combination of a small set of events that take place in vertical evolution from common ancestors. A heuristic method was proposed to solve this problem. However, no study was done to identify the complexity of the problem. Results Here, we establish that finding the homologous gene block problem is NP-hard and APX-hard. We have developed a greedy algorithm that runs in polynomial time and guarantees an O(ln⁡n) approximation. In addition, we formalize our problem as an integer linear program problem and solve it using the PuLP package and the standard CPLEX algorithm. Our exploration of several candidate operons reveals that our new method provides more optimal results than the results from the heuristic approach, and is significantly faster. Availability and implementation The software and data accompanying this paper are available under the GPLv3 and CC0 license respectively on: https://github.com/nguyenngochuy91/Relevant-Operon.

scholarly journals Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 843 ◽  
Author(s):  
Ran Zhou ◽  
David Macaya-Sanz ◽  
Jeremy Schmutz ◽  
Jerry W. Jenkins ◽  
Gerald A. Tuskan ◽  
...  
Keyword(s):  
Sex Determination ◽  
Populus Trichocarpa ◽  
Orthologous Gene ◽  
Inverted Repeats ◽  
Homologous Gene ◽  
Genomic Context ◽  
Male Individual ◽  
Long Read ◽  
Salix Purpurea ◽  
Populus Species

The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several Populus species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a Populus trichocarpa male individual. We also identified homologous gene sequences in the SDR of P. trichocarpa and the SDR of the W chromosome in Salix purpurea. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in P. trichocarpa may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.

scholarly journals A New Algorithm for Privacy-Preserving Horizontally Partitioned Linear Programs

2021 ◽  
Vol 2021 ◽  
pp. 1-4
Author(s):  
Chengxue Zhang ◽  
Debin Kong ◽  
Peng Pan ◽  
Mingyuan Zhou
Keyword(s):  
Linear Programming ◽  
Random Matrix ◽  
Optimal Solution ◽  
Full Rank ◽  
Linear Programs ◽  
Program Problem ◽  
Constraint Matrix ◽  
Right Hand ◽  
Linear Program Problem ◽  
The Matrix

In a linear programming for horizontally partitioned data, the equality constraint matrix is divided into groups of rows. Each group of the matrix rows and the corresponding right-hand side vector are owned by different entities, and these entities are reluctant to disclose their own groups of rows or right-hand side vectors. To calculate the optimal solution for the linear programming in this case, Mangasarian used a random matrix of full rank with probability 1, but an event with probability 1 is not a certain event, so a random matrix of full rank with probability 1 does not certainly happen. In this way, the solution of the original linear programming is not equal to the solution of the secure linear programming. We used an invertible random matrix for this shortcoming. The invertible random matrix converted the original linear programming problem to a secure linear program problem. This secure linear programming will not reveal any of the privately held data.

scholarly journals Syntenizer 3000: Synteny-based analysis of orthologous gene groups

2019 ◽  
Author(s):  
Camous Moslemi ◽  
Cathrine Kiel Skovbjerg ◽  
Sara Moeskjær ◽  
Stig Uggerhøj Andersen
Keyword(s):  
Sequence Similarity ◽  
Orthologous Gene ◽  
Homologous Gene ◽  
Syntenic Relationship ◽  
Gene Group ◽  
Amorphous Nature ◽  
Duplication Events ◽  
Areas Of Interest ◽  
Relationship Of

AbstractMotivationThe amorphous nature of genes combined with the prevalence of duplication events makes establishing correct genetic phylogenies challenging.Since homologous gene groups are traditionally formed on basis of sequence similarity, both orthologs and paralogs are often placed in the same gene group by existing tools. Certain tools such as PoFF take syntenic relationship of genes into consideration when forming gene groups. However, a method to form gene groups consisting of only true syntelogs has not yet been developed.In order to obtain orthologous gene groups consisting of the most likely syntelogs we need a method to filter out paralogs. If one strain has two or more copies of the same gene in a gene group we want to keep only the true syntelog in the group, and remove the paralogous copies by distinguishing between the two using synteny analysis.ResultsWe present a novel algorithm for measuring the degree of synteny shared between two genes and successfully disambiguate gene groups. This synteny measure is the basis for a number of other useful functions such as gene neighbourhood visualisation to inspect suspect gene groups, strain visualisation for assessing assembly quality and finding genomic areas of interest, and chromosome/plasmid classification of contigs in partially classified datasets.AvailabilityThe latest version of Syntenizer 3000 can be downloaded from the GitHub repository at https://github.com/kamiboy/Syntenizer3000/Consult the manual.pdf file in the repository for instructions on how to build and use the tool, as well as a in depth explanation of the algorithms utilised.

scholarly journals Exploring Students Computational Thinking based on Self-Regulated Learning in the Solution of Linear Program Problem

2019 ◽  
Vol 8 (1) ◽  
pp. 30
Author(s):  
Diah Nuraisa ◽  
Amalina Nur Azizah ◽  
Dian Nopitasari ◽  
Swasti Maharani
Keyword(s):  
Pattern Recognition ◽  
Problem Solving ◽  
Computational Thinking ◽  
Linear Program ◽  
Program Problem ◽  
Self Regulated Learning ◽  
Linear Program Problem ◽  
Regulated Learning ◽  
Depth Interviews

This study aims to analyze the students computational thinking in the solution of the linear program problem based on self-regulated learning. The data were collected by self-regulated learning questionnaire, computational thinking test, and depth interviews. This study was conducted in SMAN 10 Tangerang. Computational thinking in students with high and medium levels of self-regulated learning has no difference. Students still make a solution that is fixated with linear program problem-solving procedures in general, that is using examples, substitution, and elimination. In solving problems, students can reach the stages of decomposition and pattern recognition only. Students still do not evaluate the results of their work. Algorithmic performed is less coherent because the abstraction has not been done. The recommendation for further research is the need for research that can develop student abstraction in solving problems. Besides, there is also a need for research that analyzes the reflective of students in computational thinking when solving problems.

scholarly journals Equilibrium Pricing with Duality-Based Method: Approach for Market-Oriented Capacity Remuneration Mechanism

Energies ◽  
2021 ◽  
Vol 14 (3) ◽  
pp. 567
Author(s):  
Perica Ilak ◽  
Lin Herenčić ◽  
Ivan Rajšl ◽  
Sara Raos ◽  
Željko Tomšić
Keyword(s):  
Power System ◽  
Capacity Utilization ◽  
Case Scenario ◽  
Program Problem ◽  
Worst Case ◽  
Design Elements ◽  
Marginal Costs ◽  
Capacity Markets ◽  
Linear Program Problem

The crucial design elements of a good capacity remuneration mechanism are market orientation, insurance of long-term power system adequacy, and optimal cross-border generation capacity utilization. Having in mind these design elements, this research aims to propose a financially fair pricing mechanism that will guarantee enough new capacity and will not present state aid. The proposed capacity remuneration mechanism is an easy-to-implement linear program problem presented in its primal and dual form. The shadow prices in the primal problem and dual variables in the dual problem are used to calculate the prices of firm capacity which is capacity needed for long-term power system adequacy under capacity remuneration mechanism. In order to test if the mechanism ensures sufficient new capacity under fair prices, the mechanism is tested on the European Network of Transmission System Operators for Electricity (ENTSO-E) regional block consisting of Austria, Slovenia, Hungary, and Croatia with simulation conducted for a period of one year with a one-hour resolution and for different scenarios of the credible critical events from a standpoint of security of supply; different amounts of newly installed firm capacity; different short-run marginal costs of newly installed firm capacity; and different capacity factors of newly installed firm capacity. Test data such as electricity prices and electricity load are referred to the year 2018. The results show that the worst-case scenario for Croatia is an isolated system scenario with dry hydrology that results with high values of indicators expected energy not served (EENS), loss of load expectation (LOLE), and loss of load probability (LOLP) for Croatia. Therefore, new capacity of several hundred MW is needed to stabilize these indicators at lower values. Price for that capacity depends on the range of installed firm capacity and should be in range of 1000–7000 €/MW/year for value of lost load (VoLL) in Croatia of 1000 €/MWh and 3000–22,000 €/MW/year for VoLL of 3100 €/MWh that correlates with prices from already established capacity markets. The presented methodology can assist policymakers, regulators, and market operators when determining capacity remuneration mechanism rules and both capacity and price caps. On the other hand, it can help capacity market participants to prepare the most suitable and near-optimal bids on capacity markets.

scholarly journals Directional selection can drive the evolution of modularity in complex traits

2014 ◽  
Vol 112 (2) ◽  
pp. 470-475 ◽  
Author(s):  
Diogo Melo ◽  
Gabriel Marroig
Keyword(s):  
Complex Traits ◽  
Directional Selection ◽  
Stabilizing Selection ◽  
Simulation Framework ◽  
Full Agreement ◽  
Central Concept ◽  
Modern Biology ◽  
Living Organisms ◽  
Multivariate Systems ◽  
Evolutionary Consequences

Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection.

scholarly journals MEMAKSIMALKAN KEUNTUNGAN HARIAN PADA INDUSTRI RUMAHAN “NANDA JAYA” DENGAN PENERAPAN METODE SIMPLEKS

2020 ◽  
Vol 14 (4) ◽  
pp. 535-542
Author(s):  
Lukas Susanto
Keyword(s):  
Mathematical Model ◽  
Data Analysis ◽  
Data Collection ◽  
Simplex Method ◽  
Research Problem ◽  
Selling Price ◽  
Program Problem ◽  
Maximum Profit ◽  
Linear Program Problem ◽  
The Mathematical Model

The home industry "Nanda Jaya" produces banana chips, cassava chips and tempe chips daily. From preliminary observations, information is obtained that in determining the composition of the number of units for each type of chips produced, and determining the selling price of the product per unit, is carried out on the basis of experience while running the business, so there is no optimal way to determine it. With this condition, the company's profit needs to be reviewed whether it is optimal or not. The purpose of this research is to determine the number of production units of each type of chips, in order to obtain maximum profit and also determine the efficiency that occurs in the utilization of cost and time resources. Data collection was carried out by observation and interviews. The mathematical model of the research problem is a linear program problem with three variables that can be solved by the simplex method. From the results of data analysis, it was concluded that in order to obtain maximum profit, the company had to produce 74 units of Banana Chips, 161 units of Cassava Chips and Tempe Chips not to be produced. Maximum profit is Rp. 285,387, - (previously Rp. 247,000, -), Production Capital was reduced to Rp. 889,613, - (previously Rp. 928,000, -), while the total available time was used up.

scholarly journals Profil Kemampuan Mahasiswa Tadris Matematika dalam Memecahkan Masalah Program Linear Ditinjau dari Perbedaan Tingkat Kemampuan Prasyarat dan Gaya Kognitif Fiel Dependent

2018 ◽  
Vol 6 (1) ◽  
pp. 29-46
Author(s):  
Sitti Zuhaerah Thalhah
Keyword(s):  
Problem Solving ◽  
Cognitive Style ◽  
Linear Program ◽  
Research Subjects ◽  
Program Problem ◽  
Good Ability ◽  
Linear Program Problem ◽  
Field Dependent ◽  
Ability Tests ◽  
Simplex Methods

Abstract:This research has been carried out on Semester II students of Mathematics education Department, Faculty of Tarbiyah and Teacher Training at IAIN Palopo in 2017. The type of this research is qualitative descriptive. This research aims to describe the ability of students in solving Linear Program problems in terms of differences in the level of prerequisite ability and cognitive style. The instruments were (1) GEFT test, (2) Linear Algebra prerequisite ability tests, (3) Linear Program problem solving tests, (4) and unstructured task-based interviews. The results of this study are (1) research subjects with high prerequisite ability dependent field cognitive style, showing good ability in understanding problems correctly, planning solutions, solving problems in accordance with the plan and re-examining the results obtained. Subjects can solve Linear Program problems with graph and simplex methods (2) research subjects with prerequisite abilities while field dependent cognitive style, able to understand problems correctly, still unsure when carrying out solutions, but according to plan. Subjects can solve Linear Program problems with graphical methods and simplex methods, (3) research subjects with low prerequisite ability in field dependent cognitive style, lack of ability to understand problems, unable to carry out problem solving correctly, and unsure in explaining the completion steps taken.Abstrak: Penelitian ini dilaksanakan di IAIN Palopo Fakultas Tarbiyah dan Ilmu Pendidikan Tadris Matematika Semester III Tahun 2017. Jenis penelitian ini adalah deskriptif kualitatif. Yang bertujuan mendeskripsikan kemampuan mahasiswa dalam memecahkan masalah Program Linier ditinjau dari perbedaan tingkat kemampuan prasyarat dan gaya kognitif. Instrumen yang digunakan adalah (1) tes GEFT, (2) tes kemampuan prasyarat Aljabar Linier, (3) tes pemecahan masalah Program Linier, (4) dan wawancara berbasis tugas tidak terstruktur. Hasil penelitian ini adalah (1) subjek penelitian dengan kemampuan prasyarat tinggi gaya kognitif field dependen, menunjukkan kemampuan yang baik dalam memahami masalah dengan tepat, merencanakan pemecahan, menyelesaikan masalah sesuai dengan rencana dan memeriksa kembali hasil yang diperoleh. Subjek dapat menyelesaikan masalah Program Linier dengan metode grafik dan simpleks (2) subjek penelitian dengan kemampuan prasyarat sedang gaya kognitif field dependent, dapat memahami masalah dengan tepat, masih kurang yakin saat melaksanakan pemecahan, namun sesuai dengan rencana. Subjek dapat menyelesaikan masalah Program Linier dengan metode grafik dan metode simpleks, (3) subjek penelitian dengan kemampuan prasyarat rendah gaya kognitif field dependent, kurang mampu memahami permasalahan, tidak mampu melaksanakan pemecahan masalah dengan benar, dan tidak yakin dalam menjelaskan langkah-langkah penyelesaian yang ditempuh.

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