Phylogenies are extremely useful tools, not only for establishing genealogical relationships among a group of organisms or their parts (e.g. genes), but also variety research once the phylogenies estimated. In recent review, Pagel (1999) eloquently outline number uses phylogenetic information from discovery drug resistance to reconstructing common ancestor all life. have been used predict future trends in infectious disease ( Bush et al. 1999 ) and even offered as evidence court law Vogel...

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.

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, date, next-gen been used principally for whole transcriptome sequencing. Yet many questions population genetics systematics rely on specific genes of known function or diversity levels. Here, we describe a targeted amplicon (TAS) approach capitalizing capacity sequence large numbers gene regions from number samples. Our TAS is easily scalable,...

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...

Abstract Introgression is an important biological process affecting at least 10% of the extant species in animal kingdom. significantly impacts inference phylogenetic relationships where a strictly binary tree model cannot adequately explain reticulate net-like relationships. Here, we use phylogenomic approaches to understand patterns introgression along evolutionary history unique, nonmodel insect system: dragonflies and damselflies (Odonata). We demonstrate that pervasive force across...

Improvement of crop production is needed to feed the growing world population as amount and quality agricultural land decreases soil salinity increases. This has stimulated research on salt tolerance in plants. Most crops tolerate a limited survive produce biomass, while halophytes (salt-tolerant plants) have ability grow with saline water utilizing specific biochemical mechanisms. However, little known about genes involved tolerance. We characterized transcriptome Suaeda fruticosa,...

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...

The genetic rules that dictate legume-rhizobium compatibility have been investigated for decades, but the causes of incompatibility occurring at late stages nodulation process are not well understood. An evaluation naturally diverse legume (genus Medicago) and rhizobium Sinorhizobium) isolates has revealed numerous instances in which Sinorhizobium strains induce occupy nodules only minimally beneficial to certain Medicago hosts. Using these ineffective strain-host pairs, we identified...

Multicomputers have the potential to deliver Gigaflop performance on many scientific applications. Initial implementations of parallel programs these machines, however, are often inefficient and require significant optimization before they can harness power machine. Performance prediction tools provide valuable information which optimizations will result in increased performance. This paper describes an analytical model. The model is designed data compilers, programmers system architects...

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...

Gene duplication plays a central role in adaptation to novel environments by providing new genetic material for functional divergence and evolution of biological complexity. Several evolutionary models have been proposed gene explain how copies are preserved natural selection, but these rarely tested using empirical data. Opsin proteins, when combined with chromophore, form photopigment that is responsible the absorption light, first step phototransduction cascade. Adaptive duplications...

Accurate detection of homologous relationships biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that essential to various evolutionary studies, ranging from building phylogenies predicting functional gene annotations. There are many existing heuristic tools, most commonly based on bidirectional BLAST searches used identify genes combine them into two fundamentally distinct classes: orthologs paralogs. Due only using filtering significance...

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...

Abstract Trisomy 21 in humans causes cognitive impairment, craniofacial dysmorphology, and heart defects collectively referred to as Down syndrome. Yet, the pathophysiology of these phenotypes is not well understood. Craniofacial alterations may lead complications breathing, eating, communication. Ts65Dn mice exhibit that model syndrome including a small mandible. We show embryos at 13.5 days gestation (E13.5) have smaller mandibular precursor but normal sized tongue compared euploid...

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...

The computational cost of encryption is a barrier to wider application variety data security protocols. Virtually all research on elliptic curve cryptography (ECC) provides evidence suggest that ECC can provide family algorithms require fewer resources for implementation than do current widely used methods. This efficiency obtained since allows much shorter key lengths equivalent levels security. paper suggests how improvements in execution be by changing the representation elements finite...