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Precise genotyping and recombination detection of Enterovirus

Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception...

Subset selection of high-depth next generation sequencing reads for de novo genome assembly using MapReduce framework

Background Recent progress in next-generation sequencing technology has afforded several improvements such as ultra-high throughput at low cost, very high read quality, and substantially increased sequencing depth. State-of-the-art high-throughput sequencers, such as the Illumina MiSeq system, can generate ~15 Gbp sequencing data per run, with >80% bases above Q30 and a...

De Novo Assembly of the Whole Transcriptome of the Wild Embryo, Preleptocephalus, Leptocephalus, and Glass Eel of Anguilla japonica and Deciphering the Digestive and Absorptive Capacities during Early Development

Natural stocks of Japanese eel (Anguilla japonica) have decreased drastically because of overfishing, habitat destruction, and changes in the ocean environment over the past few decades. However, to date, artificial mass production of glass eels is far from reality because of the lack of appropriate feed for the eel larvae. In this study, wild glass eel, leptocephali...

cytoHubba: identifying hub objects and sub-networks from complex interactome

Background Network is a useful way for presenting many types of biological data including protein-protein interactions, gene regulations, cellular pathways, and signal transductions. We can measure nodes by their network features to infer their importance in the network, and it can help us identify central elements of biological networks. Results We introduce a novel Cytoscape...

The effect of red light and far-red light conditions on secondary metabolism in Agarwood

Background Agarwood, a heartwood derived from Aquilaria trees, is a valuable commodity that has seen prevalent use among many cultures. In particular, it is widely used in herbal medicine and many compounds in agarwood are known to exhibit medicinal properties. Although there exists much research into medicinal herbs and extraction of high value compounds, few have focused on...

CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce

Cloud to Chung-Yen Lin. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that ... Collaboration Projects for helping this research through the project to Chung-Yen Lin. Conceived and designed the experiments: WCC CCC JMH CYL WLH YCW DTL FL YJC. Performed the experiments: WCC CCC YCW YJC

Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena)

Background Animals co-evolve with their gut microbiota; the latter can perform complex metabolic reactions that cannot be done independently by the host. Although the importance of gut microbiota has been well demonstrated, there is a paucity of research regarding its role in foliage-foraging mammals with a specialized digestive system. Results In this study, a 16S rRNA gene...

A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles

Background Many research results show that the biological systems are composed of functional modules. Members in the same module usually have common functions. This is useful information to understand how biological systems work. Therefore, detecting functional modules is an important research topic in the post-genome era. One of functional module detecting methods is to find...

UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/ genomic level

Background Nucleic acid hybridization is an extensively adopted principle in biomedical research, in which the performance of any hybridization-based method depends on the specificity of probes to their targets. To determine the optimal probe(s) for detecting target(s) from a sample cocktail, we developed a novel algorithm, which has been implemented into a web platform for probe...

Reconstruction of human protein interolog network using evolutionary conserved network

Background The recent increase in the use of high-throughput two-hybrid analysis has generated large quantities of data on protein interactions. Specifically, the availability of information about experimental protein-protein interactions and other protein features on the Internet enables human protein-protein interactions to be computationally predicted from co-evolution events...

A Quantitative High-Resolution Genetic Profile Rapidly Identifies Sequence Determinants of Hepatitis C Viral Fitness and Drug Sensitivity

Widely used chemical genetic screens have greatly facilitated the identification of many antiviral agents. However, the regions of interaction and inhibitory mechanisms of many therapeutic candidates have yet to be elucidated. Previous chemical screens identified Daclatasvir (BMS-790052) as a potent nonstructural protein 5A (NS5A) inhibitor for Hepatitis C virus (HCV) infection...

The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays

Background Nucleic acid hybridization, a fundamental technique in molecular biology, can be modified into very effective and sensitive methods for detecting particular targets mixed with millions of non-target sequences. Therefore, avoiding cross-hybridization is the most crucial issue for developing diagnostic methods based on hybridization. Results To develop a probe with a...

PALM: A Paralleled and Integrated Framework for Phylogenetic Inference with Automatic Likelihood Model Selectors

Lin 0 Magnus Rattray, University of Manchester, United Kingdom 0 1 Institute of Information Science , Academia Sinica, Taipei, Taiwan , 2 Division of Biostatistics and Bioinformatics, National Health

Hubba: hub objects analyzer—a framework of interactome hubs identification for network biology

One major task in the post-genome era is to reconstruct proteomic and genomic interacting networks using high-throughput experiment data. To identify essential nodes/hubs in these interactomes is a way to decipher the critical keys inside biochemical pathways or complex networks. These essential nodes/hubs may serve as potential drug-targets for developing novel therapy of human...

POWER: PhylOgenetic WEb Repeater—an integrated and user-optimized framework for biomolecular phylogenetic analysis

POWER, the PhylOgenetic WEb Repeater, is a web-based service designed to perform user-friendly pipeline phylogenetic analysis. POWER uses an open-source LAMP structure and infers genetic distances and phylogenetic relationships using well-established algorithms (ClustalW and PHYLIP). POWER incorporates a novel tree builder based on the GD library to generate a high-quality tree...

Genomic shotgun array: a procedure linking large‐scale DNA sequencing with regional transcript mapping

To facilitate transcript mapping and to investigate alterations in genomic structure and gene expression in a defined genomic target, we developed a novel microarray‐based method to detect transcriptional activity of the human chromosome 4q22‐24 region. Loss of heterozygosity of human 4q22‐24 is frequently observed in hepatocellular carcinoma (HCC). One hundred and eighteen well...

Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology

Background Proteins control and mediate many biological activities of cells by interacting with other protein partners. This work presents a statistical model to predict protein interaction networks of Drosophila melanogaster based on insight into domain interactions. Results Three high-throughput yeast two-hybrid experiments and the collection in FlyBase were used as our...

hp-DPI: Helicobacter pylori Database of Protein Interactomes—embracing experimental and inferred interactions

Summary: We implemented a statistical model into our protein interaction database for validation of two-hybrid assays of Helicobacter pylori, and prediction of putative protein interactions not yet discovered experimentally. To present the enormous amount of experimental and inferred protein interaction networking maps, the H.pylori Database of Protein Interactomes (hp-DPI) is...

The Chloroplast Genome of Phalaenopsis aphrodite (Orchidaceae): Comparative Analysis of Evolutionary Rate with that of Grasses and Its Phylogenetic Implications

Whether the Amborella/Amborella-Nymphaeales or the grass lineage diverged first within the angiosperms has recently been debated. Central to this issue has been focused on the artifacts that might result from sampling only grasses within the monocots. We therefore sequenced the entire chloroplast genome (cpDNA) of Phalaenopsis aphrodite, Taiwan moth orchid. The cpDNA is a...