The release of ChIP-seq data from the ENCyclopedia Of DNA Elements (ENCODE) and Model Organism (modENCODE) projects has significantly increased amount transcription factor (TF) binding affinity information available to researchers. However, scientists still routinely use TF site (TFBS) search tools scan unannotated sequences for TFBSs, particularly when searching lesser-known TFs or in organisms which are unavailable. sequence analysis often involves multiple steps such as model collection,...

Handling genotype data typed at hundreds of thousands loci is very time-consuming and it no exception for population structure inference. Therefore, we propose to apply PCA the a population, select significant principal components using Tracy-Widom distribution, assign individuals one or more subpopulations generic clustering algorithms. We investigated K-means, soft K-means spectral made comparison STRUCTURE, model-based algorithm specifically designed Moreover, methods predicting number in...

LASAGNA-Search 2.0 is an integrated webtool for transcription factor (TF) binding site search and visualization. The tool based on the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm. It eliminates manual TF model collection promoter sequence retrieval. Search results can be visualized locally or in University of California Santa Cruz Genome Browser. Gene regulatory network inference offers another way A list TFs target genes all a user needs to start using...

Due to the significant amount of DNA data that are being generated by next-generation sequencing machines for genomes lengths ranging from megabases gigabases, there is an increasing need compress such a less space and faster transmission. Different implementations Huffman encoding incorporating characteristics sequences prove better data. These center on concepts selecting frequent repeats so as force skewed tree, well construction multiple trees when encoding. The demonstrate improvements...

The demand for indoor localization services in the Internet of Things (IoT) has been increasing dramatically during last decade. Many systems adopt Wi-Fi fingerprinting with received signal strength indicators (RSSIs) as a source sensors to localize an object because it is cost effective and can give high accuracy. However, fluctuation wireless signals resulting from environmental uncertainties leads considerable variations RSSIs, which poses challenge accurate on single floor, not mention...

DNA Microarray technology is an innovative methodology in experimental molecular biology, which has produced huge amounts of valuable data the profile gene expression. Many clustering algorithms have been proposed to analyze expression data, but little guidance available help choose among them. The evaluation feasible and applicable becoming important issue today's bioinformatics research. In this paper we first experimentally study three major algorithms: Hierarchical Clustering (HC),...

Scientists routinely scan DNA sequences for transcription factor (TF) bindingsites (TFBSs). Most of the available tools rely on position-specific scoringmatrices (PSSMs) constructed from aligned binding sites. Because theresolutions assays used to obtain TFBSs, databases such as TRANSFAC,ORegAnno and PAZAR store unaligned variable-length segments containingbinding sites a TF. These need be build aPSSM. While TRANSFAC database provides scoring matrices TFs, nearly78% TFs in public release do...

The location-based services for Internet of Things (IoTs) have attracted extensive research effort during the last decades. Wi-Fi fingerprinting with received signal strength indicator (RSSI) has been widely adopted in vast indoor localization systems due to its relatively low cost and potency high accuracy. However, fluctuation wireless resulting from environment uncertainties leads considerable variations on RSSIs, which poses grand challenges fingerprint-based regarding positioning In...

The detection of network motifs has recently become an important part analysis across all disciplines. In this work, we detected and analyzed from undirected directed networks several different disciplines, including biological network, social ecological as well other such airlines, power grid, co-purchase political books networks. Our revealed that are similar at the basic three four nodes, while distinction between study showed larger contained three-node motif a subgraph. Topological have...

Computational approaches to transcription factor binding site identification have been actively researched in the past decade. Learning from known sites, new sites of a unannotated sequences can be identified. A number search methods introduced over years. However, one rarely find single method that performs best on all factors. Instead, identify for particular factor, usually has compare handful methods. Hence, it is highly desirable perform automatic optimization individual We proposed...

Nowadays, traditional networks are suffering from lack of information, easy management, and hard QoS guarantee. Recently, SDNs overcome these limitations. They provide network agility, programmability, centralized control. These features facilitate solving many the security, performance, management issues. In this paper, we propose an SDN framework that leverages programmability control to a level QoS. Knowing state whole helps optimizing decision towards enhancing efficiency. The presented...

The cost-effectiveness of next-generation sequencing (NGS) has led to the advancement genomic research, thereby regularly generating a large amount raw data that often requires efficient infrastructures such as centers manage storage and transmission data. generated NGS are highly redundant need be efficiently compressed reduce cost space bandwidth. We present lossless, non-reference-based FASTQ compression algorithm, known LFastqC, an improvement over LFQC tool, address these issues....

Next-generation sequencing technologies are producing genomic data at ever-increasing rates. It has become a challenge to store, transmit, and process the massive quantity of data, creating vital need for tool that compresses produced in lossless manner, thus reducing storage space speeding up transmission. Data centers adopting either two general-purpose compressors: gzip or bzip2. Both these use Huffman encoding, although they implement it different ways. However, neither takes advantage...

The steady natural convection along an inclined stretching surface in the presence of chemical reaction under thermal-diffusion and diffusion-thermo effects is studied. governing equations for continuity, momentum, energy, concentration are transformed by similarity transformation then solved numerically using Runge-Kutta integration with shooting scheme. Comparisons between present data previously published work performed found to be very good agreement each other. obtained results show...

Software-Defined Networking (SDN) is an emerging technology that supports recent network applications. An SDN redefines networks by introducing the concept of decoupling control plane from data plane, thus providing centralized management, programmability, and dynamic reconfiguration. In this research, we specifically investigate significance using SDNs in support Big-Data proved to applications through a more efficient use distributed nodes. With Hadoop as example application, performance...

The dimensionality of the spatially distributed channels and temporal resolution electroencephalogram (EEG) based brain-computer interfaces (BCI) undermine emotion recognition models. Thus, prior to modeling such data, as final stage learning pipeline, adequate preprocessing, transforming, extracting (i.e., time-series signals) spatial electrode channels) features are essential phases recognize underlying human emotions. Conventionally, inter-subject variations dealt with by avoiding sources...

Significant research effort has been made on formulating new topologies to meet the requirements of current and future large-scale data centers. Nowadays centers may include tens thousands servers, leading an urgent need for higher bandwidth, better reliability, easier management lower latency. This paper investigates potential using software-defined networks (SDNs) in Extreme scale systems, which are required when scaling up Exascale level. SDN is trend efficient traffic control network...