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https://www.readbyqxmd.com/read/28079128/parallel-meta-3-comprehensive-taxonomical-and-functional-analysis-platform-for-efficient-comparison-of-microbial-communities
#1
Gongchao Jing, Zheng Sun, Honglei Wang, Yanhai Gong, Shi Huang, Kang Ning, Jian Xu, Xiaoquan Su
The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28076851/pse-analysis-a-python-package-for-dna-rna-and-protein-peptide-sequence-analysis-based-on-pseudo-components-and-kernel-methods
#2
Bin Liu, Hao Wu, Deyuan Zhang, Xiaolong Wang, Kuo-Chen Chou
To expedite the pace in conducting genome/proteome analysis, we have developed a Python package called Pse-Analysis. The powerful package can automatically complete the following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3) model training, (4) cross validation, and (5) evaluating prediction quality. All the work a user needs to do is to input a benchmark dataset along with the query biological sequences concerned. Based on the benchmark dataset, Pse-Analysis will automatically construct an ideal predictor, followed by yielding the predicted results for the submitted query samples...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28069593/knime4ngs-a-comprehensive-toolbox-for-next
#3
Maximilian Hastreiter, Tim Jeske, Jonathan Hoser, Michael Kluge, Kaarin Ahomaa, Marie-Sophie Friedl, Sebastian J Kopetzky, Jan-Dominik Quell, H- Werner Mewes, Robert Küffner
: Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis...
January 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28064377/octopus-a-platform-for-the-virtual-high-throughput-screening-of-a-pool-of-compounds-against-a-set-of-molecular-targets
#4
Eduardo Habib Bechelane Maia, Vinícius Alves Campos, Bianca Dos Reis Santos, Marina Santos Costa, Iann Gabriel Lima, Sandro J Greco, Rosy I M A Ribeiro, Felipe M Munayer, Alisson Marques da Silva, Alex Gutterres Taranto
Octopus is an automated workflow management tool that is scalable for virtual high-throughput screening (vHTS). It integrates MOPAC2016, MGLTools, PyMOL, and AutoDock Vina. In contrast to other platforms, Octopus can perform docking simulations of an unlimited number of compounds into a set of molecular targets. After generating the ligands in a drawing package in the Protein Data Bank (PDB) format, Octopus can carry out geometry refinement using the semi-empirical method PM7 implemented in MOPAC2016. Docking simulations can be performed using AutoDock Vina and can utilize the Our Own Molecular Targets (OOMT) databank...
January 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28062442/sine_scan-an-efficient-tool-to-discover-short-interspersed-nuclear-elements-sines-in-large-scale-genomic-datasets
#5
Hongliang Mao, Hao Wang
MOTIVATION: Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. RESULTS: Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element...
January 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28043542/the-analysis-of-exosomal-micro-rnas-in-peripheral-blood-mononuclear-cell-derived-macrophages-after-infection-with-bacillus-calmette-gu%C3%A3-rin-by-rna-sequencing
#6
Esmaeil Mortaz, Shamila D Alipoor, Payam Tabarsi, Ian M Adcock, Johan Garssen, Ali Akbar Velayati
OBJECTIVE/BACKGROUND: Tuberculosis (TB) is a major global threat to human health, especially in low-income countries. The diagnosis of TB is challenging because of the limitations of specificity and sensitivity with the current diagnostics. Novel, selective biomarkers for TB would be of great practical value. Exosomes are bioactive vesicles with 30-100nm in diameter, which are secreted from almost all cell types and are found in virtually every human body fluid. Exosomes transport micro-RNAs (miRNAs), which are post-transcriptional regulators of gene expression, around the body and allow miRNAs to modulate biological pathways in target cells...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28028736/fast-h-drop-a-thirty-times-accelerated-version-of-h-drop-for-interactive-svm-based-prediction-of-helical-domain-linkers
#7
Tambi Richa, Soichiro Ide, Ryosuke Suzuki, Teppei Ebina, Yutaka Kuroda
Efficient and rapid prediction of domain regions from amino acid sequence information alone is often required for swift structural and functional characterization of large multi-domain proteins. Here we introduce Fast H-DROP, a thirty times accelerated version of our previously reported H-DROP (Helical Domain linker pRediction using OPtimal features), which is unique in specifically predicting helical domain linkers (boundaries). Fast H-DROP, analogously to H-DROP, uses optimum features selected from a set of 3000 ones by combining a random forest and a stepwise feature selection protocol...
December 27, 2016: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28013191/partitionfinder-2-new-methods-for-selecting-partitioned-models-of-evolution-for-molecular-and-morphological-phylogenetic-analyses
#8
Robert Lanfear, Paul B Frandsen, April M Wright, Tereza Senfeld, Brett Calcott
PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems...
December 23, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28011776/sarconfocal-simultaneous-sarcomere-length-and-cytoplasmic-calcium-measurements-for-laser-scanning-confocal-microscopy-images
#9
Côme Pasqualin, François Gannier, Angèle Yu, Claire O Malécot, Pierre Bredeloux, Véronique Maupoil
: Simultaneous recordings of myocytes contractility and their cytoplasmic calcium concentration allow powerful studies, particularly on heart failure and other cardiac dysfunctions. Such studies require dedicated and expensive experimental devices that are difficult to use. Thus we propose SarConfoCal, the first and only software to simultaneously analyse both cytoplasmic calcium variations (from fluorescence signal) and myocytes contractility (from sarcomere length measurement) on laser scanning confocal microscopy images...
December 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28011768/seqlib-a-c%C3%A2-api-for-rapid-bam-manipulation-sequence-alignment-and-sequence-assembly
#10
Jeremiah Wala, Rameen Beroukhim
: We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM...
December 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28003266/gwalpha-genome-wide-estimation-of-additive-effects-alpha-based-on-trait-quantile-distribution-from-pool-sequencing-experiments
#11
Alexandre Fournier-Level, Charles Robin, David J Balding
MOTIVATION: Sequencing pools of individuals (Pool-Seq) is a cost-effective way to gain insight into the genetics of complex traits, but as yet no parametric method has been developed to both test for genetic effects and estimate their magnitude. Here, we propose GWAlpha, a flexible method to obtain parametric estimates of genetic effects genome-wide from Pool-Seq experiments. RESULTS: We showed that GWAlpha powerfully replicates the results of GWAS from model organisms...
December 21, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27993787/improved-vcf-normalization-for-accurate-vcf-comparison
#12
Arash Bayat, Bruno Gaëta, Aleksandar Ignjatovic, Sri Parameswaran
MOTIVATION: The Variant Call Format (VCF) is widely used to store data about genetic variation. Variant calling workflows detect potential variants in large numbers of short sequence reads generated by DNA sequencing and report them in VCF format. To evaluate the accuracy of variant callers, it is critical to correctly compare their output against a reference VCF file containing a gold standard set of variants. However, comparing VCF files is a complicated task as an individual genomic variant can be represented in several different ways and is therefore not necessarily reported in a unique way by different software...
December 19, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27943406/fast-genome-wide-qtl-association-mapping-on-pedigree-and-population-data
#13
Hua Zhou, John Blangero, Thomas D Dyer, Kei-Hang K Chan, Kenneth Lange, Eric M Sobel
Since most analysis software for genome-wide association studies (GWAS) currently exploit only unrelated individuals, there is a need for efficient applications that can handle general pedigree data or mixtures of both population and pedigree data. Even datasets thought to consist of only unrelated individuals may include cryptic relationships that can lead to false positives if not discovered and controlled for. In addition, family designs possess compelling advantages. They are better equipped to detect rare variants, control for population stratification, and facilitate the study of parent-of-origin effects...
December 12, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/27932907/optimized-r-functions-for-analysis-of-ecological-community-data-using-the-r-virtual-laboratory-rvlab
#14
Constantinos Varsos, Theodore Patkos, Anastasis Oulas, Christina Pavloudi, Alexandros Gougousis, Umer Zeeshan Ijaz, Irene Filiopoulou, Nikolaos Pattakos, Edward Vanden Berghe, Antonio Fernández-Guerra, Sarah Faulwetter, Eva Chatzinikolaou, Evangelos Pafilis, Chryssoula Bekiari, Martin Doerr, Christos Arvanitidis
BACKGROUND: Parallel data manipulation using R has previously been addressed by members of the R community, however most of these studies produce ad hoc solutions that are not readily available to the average R user. Our targeted users, ranging from the expert ecologist/microbiologists to computational biologists, often experience difficulties in finding optimal ways to exploit the full capacity of their computational resources. In addition, improving performance of commonly used R scripts becomes increasingly difficult especially with large datasets...
2016: Biodiversity Data Journal
https://www.readbyqxmd.com/read/27920488/evalmsa-a-program-to-evaluate-multiple-sequence-alignments-and-detect-outliers
#15
Alvaro Chiner-Oms, Fernando González-Candelas
We present EvalMSA, a software tool for evaluating and detecting outliers in multiple sequence alignments (MSAs). This tool allows the identification of divergent sequences in MSAs by scoring the contribution of each row in the alignment to its quality using a sum-of-pair-based method and additional analyses. Our main goal is to provide users with objective data in order to take informed decisions about the relevance and/or pertinence of including/retaining a particular sequence in an MSA. EvalMSA is written in standard Perl and also uses some routines from the statistical language R...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27919220/deepqa-improving-the-estimation-of-single-protein-model-quality-with-deep-belief-networks
#16
Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
BACKGROUND: Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model pool consisting of mostly low-quality models, is still a largely unsolved problem. RESULTS: We introduce a novel single-model quality assessment method DeepQA based on deep belief network that utilizes a number of selected features describing the quality of a model from different perspectives, such as energy, physio-chemical characteristics, and structural information...
December 5, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27918597/seqplots-interactive-software-for-exploratory-data-analyses-pattern-discovery-and-visualization-in-genomics
#17
Przemyslaw Stempor, Julie Ahringer
Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA sequencing to assess gene expression changes after biological perturbations. To investigate the pattern and abundance of coverage signals across regions of interest, data are often visualized as profile plots of average signal or stacked rows of signal in the form of heatmaps...
2016: Wellcome Open Res
https://www.readbyqxmd.com/read/27899692/jenkins-ci-an-open-source-continuous-integration-system-as-a-scientific-data-and-image-processing-platform
#18
Ioannis K Moutsatsos, Imtiaz Hossain, Claudia Agarinis, Fred Harbinski, Yann Abraham, Luc Dobler, Xian Zhang, Christopher J Wilson, Jeremy L Jenkins, Nicholas Holway, John Tallarico, Christian N Parker
High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS)...
November 29, 2016: Journal of Biomolecular Screening
https://www.readbyqxmd.com/read/27884103/amplimethprofiler-a-pipeline-for-the-analysis-of-cpg-methylation-profiles-of-targeted-deep-bisulfite-sequenced-amplicons
#19
Giovanni Scala, Ornella Affinito, Domenico Palumbo, Ermanno Florio, Antonella Monticelli, Gennaro Miele, Lorenzo Chiariotti, Sergio Cocozza
BACKGROUND: CpG sites in an individual molecule may exist in a binary state (methylated or unmethylated) and each individual DNA molecule, containing a certain number of CpGs, is a combination of these states defining an epihaplotype. Classic quantification based approaches to study DNA methylation are intrinsically unable to fully represent the complexity of the underlying methylation substrate. Epihaplotype based approaches, on the other hand, allow methylation profiles of cell populations to be studied at the single molecule level...
November 25, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27801969/high-performance-computation-of-landscape-genomic-models-including-local-indicators-of-spatial-association
#20
S Stucki, P Orozco-terWengel, B R Forester, S Duruz, L Colli, C Masembe, R Negrini, E Landguth, M R Jones, M W Bruford, P Taberlet, S Joost
With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics-i.e. the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present Samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental datasets...
November 1, 2016: Molecular Ecology Resources
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