Phylogentic analysis is becoming an increasingly important tool for customized drug treatments, epidemiological studies, and evolutionary analysis. The TCS method provides dealing with genes at a population level. Existing software takes unreasonable amount of time the significant numbers Taxa. This paper presents algorithms describes initial attempts parallelization. Performance results are also presented algorithm on several data sets.

Emerging next-generation sequencing technologies have revolutionized the collection of genomic data for applications in bioforensics, biosurveillance, and use clinical settings. However, to make most these new data, methodology needs be developed that can accommodate large volumes genetic a computationally efficient manner. We present statistical framework analyze raw sequence reads from purified or mixed environmental targeted infected tissue samples rapid species identification strain...

The advent of next-generation sequencing technologies has increased the accuracy and quantity sequence data, opening door to greater opportunities in genomic research.In this article, we present GNUMAP (Genomic Next-generation Universal MAPper), a program capable overcoming two major obstacles mapping reads from runs. First, have created an algorithm that probabilistically maps repeat regions genome on quantitative basis. Second, developed probabilistic Needleman-Wunsch which utilizes...

Bullying, encompassing physical, psychological, social, or educational harm, affects approximately 1 in 20 United States teens aged 12-18. The prevalence and impact of bullying, including online necessitate a deeper understanding risk protective factors to enhance prevention efforts. This study investigated the key most highly associated with adolescent bullying victimization. Data from Student Health Risk Prevention (SHARP) survey, collected 345,506 student respondents Utah 2009 2021, were...

<sec> <title>BACKGROUND</title> In an era marked by the blooming reliance on digital platforms for healthcare consultation, subreddit r/AskDocs has emerged as a pivotal forum. However, vast, unstructured nature of forum data presents formidable challenge; extraction and meaningful analysis such require advanced tools that can navigate complexities language context inherent in user-generated content. </sec> <title>OBJECTIVE</title> Our objective was to evaluate employing Large Language Models...

Abstract Motivation: Multiple sequence alignments (MSAs) are at the heart of bioinformatics analysis. Recently, a number multiple protein alignment benchmarks (i.e. BAliBASE, OXBench, PREFAB and SMART) have been released to evaluate new existing MSA applications. These databases well received by researchers help quantitatively programs on sequences. Unfortunately, analogous DNA not available, making evaluation difficult for Results: This work presents first known that (1) comprised...

Introduction Addressing the problem of suicidal thoughts and behavior (STB) in adolescents requires understanding associated risk factors. While previous research has identified individual protective factors with many adolescent social morbidities, modern machine learning approaches can help identify that interact (group) to provide predictive power for STB. This study aims develop a prediction algorithm STB among using factor framework determinants health. Methods The sample population...

The computing community has long faced the problem of scientifically comparing different computers and algorithms. When architectures, methods, precision, or storage capacity are very it is difficult misleading to compare speeds using ratio execution times. We present a practical fair approach that provides mathematically sound comparison computational performance even when algorithm, computer, precision changed. HINT (Hierarchical INTegration) removes need for pseudo-work measures such as...

Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data the complexity present a challenge obtaining results timely manner. Known methods to accelerate on reconfigurable hardware only address comparison, limit length, or exhibit memory I/O bottlenecks. A space‐efficient, global algorithm architecture presented that accelerates forward scan traceback without limitations. With 256 processing elements FPGA...

Genome assemblers to date have predominantly targeted haploid reference reconstruction from homozygous data. When applied diploid genome assembly, these perform poorly, owing the violation of assumptions during both contigging and scaffolding phases. Effective tools overcome problems are in growing demand. Increasing parameter stringency is an effective solution obtaining haplotype-specific contigs; however, algorithms for such contigs lacking.We present a stand-alone algorithm,...

Article Design issues for efficient implementation of MPI in Java Share on Authors: Glenn Judd Computer Science Department, Brigham Young University, Provo ProvoView Profile , Mark Clement Quinn Snell Vladimir Getov School Science, University Westminster, London, UK UKView Authors Info & Claims JAVA '99: Proceedings the ACM 1999 conference GrandeJune Pages 58–65https://doi.org/10.1145/304065.304097Online:01 June 1999Publication History 28citation1,393DownloadsMetricsTotal Citations28Total...

The performance of Java just-in-time compilers currently approaches native C++, making a serious contender for supercomputing application development. This paper presents DOGMA – new based system which enables parallel computing on heterogeneous computers. supports programming in both traditional message-passing form and novel object-oriented approach. provides support dedicated clusters as well idle workstations through the use web-based browse-in feature or screen saver. research unified...

Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive consequently exhibit performance limitations according to Amdahl's Law. This work known accelerate third on hardware.We reduce subgroups aligned sequences into discrete profiles before they are pairwise accelerator. Using an FPGA accelerator, overall...

Error correction is an important step in increasing the quality of next-generation sequencing data for downstream analysis and use. Polymorphic datasets are a challenge many bioinformatic software packages that designed or assume homozygosity input dataset. This assumption ignores true genomic composition organisms diploid polyploid. In this survey, two different error packages, Quake ECHO, examined to see how they perform on sequence from heterozygous genomes. ECHO well were able correct...

Long branch attraction (LBA) is a problem that afflicts both the parsimony and maximum likelihood phylogenetic analysis techniques. Research has shown particularly vulnerable to inferring wrong tree in Felsenstein topologies. The long extraction method procedure detect data set suffering from this so Maximum Likelihood could be used instead of Parsimony. been well cited by many authors their but no strong validation performed as its accuracy. We such an extensive search length space under...

Finding a team that is both competent in performing the task and compatible working together has been extensively studied. However, most methods for formation tend to rely on set of skills only. In order solve this problem, we present an efficient method based Constrained Pattern Graph (called CPG). Unlike traditional methods, our takes into account structure constraints communication members, which can better meet requirements users. First, CPG preprocessing proposed normalize represent it...

The contig orientation problem, which we formally define as the MAX-DIR has at times been addressed cursorily and using various heuristics. In setting forth a linear-time reduction from MAX-CUT problem to prove latter is NP-complete. We compare relative performance of novel greedy approach with several other heuristic solutions.Our results suggest that our algorithm not only works well but also outperforms algorithms due nature scaffold graphs. Our demonstrate method for identifying inverted...

Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data the complexity present a challenge obtaining results timely manner. Known methods to accelerate on reconfigurable hardware only address comparison, limit length, or exhibit memory I/O bottlenecks. A space-efficient, global algorithm architecture presented that accelerates forward scan traceback without limitations. With 256 processing elements FPGA...

Mapping short next-generation reads to reference genomes is an important element in SNP calling and expression studies. A major limitation large-scale whole-genome mapping the large memory requirements for algorithm long run-time necessary accurate Several parallel implementations have been performed distribute on different processors equally share processing requirements. These approaches are compared with respect their footprint, load balancing, accuracy. When using MPI multi-threading,...

Abstract Background DNA methylation has been linked to many important biological phenomena. Researchers have recently begun sequence bisulfite treated determine its pattern of methylation. However, sequencing reads from bisulfite-converted can vary significantly the reference genome because incomplete conversion, variation, errors, and poor quality bases. Therefore, it is often difficult align correct locations in genome. Furthermore, experiments additional complexity having estimate levels...

Before implementing scheduling policies (i.e. job prioritization) on a system, it is imperative that their effects performance be understood. Changing without this knowledge may result in issues such as starvation, increased queue time, and decreased system utilization. This paper proposes means of reproducibly accurately determining the true impact changes policy, resource configuration, workload distribution. The proposed solution, Maui Scheduler possesses an advanced, easy-to-use,...