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Tasnia Tahsin, Davy Weissenbacher, Karen O'Connor, Arjun Magge, Matthew Scotch, Graciela Gonzalez-Hernandez
Summary: GeoBoost is a command-line software package developed to address sparse or incomplete metadata in GenBank sequence records that relate to the location of the infected host (LOIH) of viruses. Given a set of GenBank accession numbers corresponding to virus GenBank records, GeoBoost extracts, integrates, and normalizes geographic information reflecting the LOIH of the viruses using integrated information from GenBank metadata and related full-text publications. In addition, to facilitate probabilistic geospatial modeling, GeoBoost assigns probability scores for each possible LOIH...
December 12, 2017: Bioinformatics
Mattia Chiesa, Gualtiero I Colombo, Luca Piacentini
Summary: RNA-Seq is becoming the technique of choice for high-throughput transcriptome profiling, which, besides class comparison for differential expression, promises to be an effective and powerful tool for biomarker discovery. However, a systematic analysis of high-dimensional genomic data is a demanding task for such a purpose. DaMiRseq offers an organized, flexible and convenient framework to remove noise and bias, select the most informative features and perform accurate classification...
December 11, 2017: Bioinformatics
Ehsan Samei, Lynda C Ikejimba, Brian P Harrawood, John Rong, Ian A Cunningham, Michael J Flynn
PURPOSE: The AAPM Task Group 162 aimed to provide a standardized approach for the assessment of image quality in planar imaging systems. This report offers a description of the approach as well as the details of the resultant software bundle to measure detective quantum efficiency (DQE) as well as its basis components and derivatives. METHODS: The methodology and the associated software include the characterization of the noise power spectrum (NPS) from planar images acquired under specific acquisition conditions, modulation transfer function (MTF) using an edge test object, the DQE, and effective DQE (eDQE)...
December 8, 2017: Medical Physics
Osvaldo Graña, Hugo López-Fernández, Florentino Fdez-Riverola, David González Pisano, Daniel Glez-Peña
Summary: High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data...
December 1, 2017: Bioinformatics
John M Gaspar, Ronald P Hart
BACKGROUND: DNA methylation is an epigenetic modification that is studied at a single-base resolution with bisulfite treatment followed by high-throughput sequencing. After alignment of the sequence reads to a reference genome, methylation counts are analyzed to determine genomic regions that are differentially methylated between two or more biological conditions. Even though a variety of software packages is available for different aspects of the bioinformatics analysis, they often produce results that are biased or require excessive computational requirements...
November 29, 2017: BMC Bioinformatics
Pierre Lindenbaum, Richard Redon
Motivation: Reformatting and filtering bioinformatics files are common tasks for bioinformaticians. Standard linux tools and specific programs are usually used to perform such tasks but there is still a gap between using these tools and the programming interface of some existing libraries. Results: In this context, we wrote a set of tools named bioalcidae, samjs and vcffilterjs that reformat or filter files using a javascript engine or a pure java expression and taking advantage of the java API for high-throughput sequencing data (htsjdk)...
November 24, 2017: Bioinformatics
Pu-Feng Du, Wei Zhao, Yang-Yang Miao, Le-Yi Wei, Likun Wang
With the avalanche of biological sequences in public databases, one of the most challenging problems in computational biology is to predict their biological functions and cellular attributes. Most of the existing prediction algorithms can only handle fixed-length numerical vectors. Therefore, it is important to be able to represent biological sequences with various lengths using fixed-length numerical vectors. Although several algorithms, as well as software implementations, have been developed to address this problem, these existing programs can only provide a fixed number of representation modes...
November 14, 2017: International Journal of Molecular Sciences
Michael L Richardson, Behrang Amini
OBJECTIVES: The goal of this article is to introduce the concept of scientific notebook software, and to illustrate how it can be used to document a research project, to perform image analysis and to create interactive teaching tools. METHODS: We describe the installation of scientific notebook software known as Project Jupyter, which is free, open-source and available for the Macintosh, Windows and Linux operating systems. RESULTS: We have created 2 scientific notebooks that demonstrate applications germane to radiologists, particularly those in academic radiology...
September 18, 2017: Current Problems in Diagnostic Radiology
Yasuhiro Tanizawa, Takatomo Fujisawa, Yasukazu Nakamura
Summary: We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes...
November 2, 2017: Bioinformatics
Toshikazu Kuroda
Remote control over devices for experiments may increase the efficiency of operant research and expand the area where behavior can be studied. This article introduces a combination of Raspberry Pi® (Pi) and SoftEther VPN® that allows for such remote control via the Internet. The Pi is a small Linux computer with a great degree of flexibility for customization. Test results indicate that a Pi-based interface meets the requirement for conducting operant research. SoftEther VPN® allows for establishing an extensive private network on the Internet using a single private Wi-Fi router...
November 1, 2017: Journal of the Experimental Analysis of Behavior
Xuhua Xia
Two major stumbling blocks exist in high-throughput sequencing (HTS) data analysis. The first is the sheer file size typically in gigabytes when uncompressed, causing problems in storage, transmission and analysis. However, these files do not need to be so large and can be reduced without loss of information. Each HTS file, either in compressed .SRA or plain text .fastq format, contains numerous identical reads stored as separate entries. For example, among 44603541 forward reads in the SRR4011234.sra file (from a Bacillus subtilis transcriptomic study) deposited at NCBI's SRA database, one read has 497027 identical copies...
October 27, 2017: G3: Genes—Genomes—Genetics
Lianming Du, Chi Zhang, Qin Liu, Xiuyue Zhang, Bisong Yue
Summary: Microsatellites are found to be related with various diseases and widely used in population genetics as genetic markers. However, it remains a challenge to identify microsatellite from large genome and screen microsatellites for primer design from a huge result dataset. Here, we present Krait, a robust and flexible tool for fast investigation of microsatellites in DNA sequences. Krait is designed to identify all types of perfect or imperfect microsatellites on a whole genomic sequence, and is also applicable to identification of compound microsatellites...
October 18, 2017: Bioinformatics
Ignacio Faustino, S J Marrink
Summary: We introduce cgHeliParm, a python program that provides the conformational analysis of Martini-based coarse-grained double strand DNA molecules. The software calculates the helical parameters such as base, base pair and base pair step parameters. cgHeliParm can be used for the analysis of coarse grain Martini molecular dynamics trajectories without transformation into atomistic models. Availability and implementation: This package works with Python 2.7 on MacOS and Linux...
July 13, 2017: Bioinformatics
Ravi José Tristão Ramos, Allan Cézar de Azevedo Martins, Gabrielle da Silva Delgado, Crina-Maria Ionescu, Turán Peter Ürményi, Rosane Silva, Jaroslav Koca
Summary: CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss...
November 15, 2017: Bioinformatics
Marek Kochanczyk, William S Hlavacek, Tomasz Lipniacki
Summary: Rule-based modeling is a powerful approach for studying biomolecular site dynamics. Here, we present SPATKIN, a general-purpose simulator for rule-based modeling in two spatial dimensions. The simulation algorithm is a lattice-based method that tracks Brownian motion of individual molecules and the stochastic firing of rule-defined reaction events. Because rules are used as event generators, the algorithm is network-free, meaning that it does not require to generate the complete reaction network implied by rules prior to simulation...
November 15, 2017: Bioinformatics
Francisco Pinho, João Cerqueira, José Correia, Nuno Sousa, Nuno Dias
The World Health Organisation has pointed that a successful health care delivery, requires effective medical devices as tools for prevention, diagnosis, treatment and rehabilitation. Several studies have concluded that longer monitoring periods and outpatient settings might increase diagnosis accuracy and success rate of treatment selection. The long-term monitoring of epileptic patients through electroencephalography (EEG) has been considered a powerful tool to improve the diagnosis, disease classification, and treatment of patients with such condition...
October 10, 2017: Journal of Medical Engineering & Technology
Manmohan Pandey, Ravindra Kumar, Prachi Srivastava, Suyash Agarwal, Shreya Srivastava, N S Nagpure, J K Jena, Basdeo Kushwaha
Mining and characterization of SSR markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. WGS-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, ncRNA, core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic and core gene region) along with primer identification and mining of cross-species markers...
September 16, 2017: Journal of Heredity
Alejandro F Villaverde, Kolja Becker, Julio R Banga
Inferring the structure of unknown cellular networks is a main challenge in computational biology. Data-driven approaches based on information theory can determine the existence of interactions among network nodes automatically. However, the elucidation of certain features - such as distinguishing between direct and indirect interactions or determining the direction of a causal link - requires estimating information-theoretic quantities in a multidimensional space. This can be a computationally demanding task, which acts as a bottleneck for the application of elaborate algorithms to large-scale network inference problems...
October 4, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Luciano Porto Kagami, Gustavo Machado das Neves, Alan Wilter Sousa da Silva, Rafael Andrade Caceres, Daniel Fábio Kawano, Vera Lucia Eifler-Lima
To speed up the drug-discovery process, molecular dynamics (MD) calculations performed in GROMACS can be coupled to docking simulations for the post-screening analyses of large compound libraries. This requires generating the topology of the ligands in different software, some basic knowledge of Linux command lines, and a certain familiarity in handling the output files. LiGRO-the python-based graphical interface introduced here-was designed to overcome these protein-ligand parameterization challenges by allowing the graphical (non command line-based) control of GROMACS (MD and analysis), ACPYPE (ligand topology builder) and PLIP (protein-binder interactions monitor)-programs that can be used together to fully perform and analyze the outputs of complex MD simulations (including energy minimization and NVT/NPT equilibration)...
October 4, 2017: Journal of Molecular Modeling
Carl D Christensen, Jan-Hendrik S Hofmeyr, Johann M Rohwer
Summary: PySCeSToolbox is an extension to the Python Simulator for Cellular Systems (PySCeS) that includes tools for performing generalised supply-demand analysis, symbolic metabolic control analysis, and a framework for investigating the kinetic and thermodynamic aspects of enzyme-catalysed reactions. Each tool addresses a different aspect of metabolic behaviour, control, and regulation; the tools complement each other and can be used in conjunction to better understand higher-level system behaviour...
September 14, 2017: Bioinformatics
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