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Bioinformatics python

Jin Zhang, Elaine R Mardis, Christopher A Maher
MOTIVATION: While high-throughput sequencing (HTS) has been used successfully to discover tumor-specific mutant peptides (neoantigens) from somatic missense mutations, the field currently lacks a method for identifying which gene fusions may generate neoantigens. RESULTS: We demonstrate the application of our gene fusion neoantigen discovery pipeline, called INTEGRATE-Neo, by identifying gene fusions in prostate cancers that may produce neoantigens. AVAILABILITY: INTEGRATE-Neo is implemented in C++ and Python...
October 24, 2016: Bioinformatics
Ahmed Arslan, Vera van Noort
: Recent advances in sequence technology result in large datasets of sequence variants. For the human genome, several tools are available to predict the impact of these variants on gene and protein functions. However, for model organisms such as yeast such tools are lacking, specifically to predict the effect of protein sequence altering variants on the protein level. We present a python framework that enables users to map in a fully automated fashion large set of variants to protein functional regions and post-translationally modified residues...
October 22, 2016: Bioinformatics
Jaroslaw Surkont, Yoan Diekmann, José B Pereira-Leal
: The Rab family of small GTPases regulates and provides specificity to the endomembrane trafficking system; each Rab subfamily is associated with specific pathways. Thus, characterization of Rab repertoires provides functional information about organisms and evolution of the eukaryotic cell. Yet, the complex structure of the Rab family limits the application of existing methods for protein classification. Here, we present a major redesign of the Rabifier, a bioinformatic pipeline for detection and classification of Rab GTPases...
October 22, 2016: Bioinformatics
Blake L Joyce, Asher Haug-Baltzell, Sean Davey, Matthew Bomhoff, James C Schnable, Eric Lyons
: Following polyploidy events, genomes undergo massive reduction in gene content through a process known as fractionation. Importantly, the fractionation process is not always random, and a bias as to which homeologous chromosome retains or loses more genes can be observed in some species. The process of characterizing whole genome fractionation requires identifying syntenic regions across genomes followed by post-processing of those syntenic datasets to identify and plot gene retention patterns...
October 29, 2016: Bioinformatics
Jorge Álvarez-Jarreta, Eduardo Ruiz-Pesini
BACKGROUND: Molecular evolution studies involve many different hard computational problems solved, in most cases, with heuristic algorithms that provide a nearly optimal solution. Hence, diverse software tools exist for the different stages involved in a molecular evolution workflow. RESULTS: We present MEvoLib, the first molecular evolution library for Python, providing a framework to work with different tools and methods involved in the common tasks of molecular evolution workflows...
October 28, 2016: BMC Bioinformatics
Shi-Yi Chen, Feilong Deng, Ying Huang, Cao Li, Linhai Liu, Xianbo Jia, Song-Jia Lai
Although various computer tools have been elaborately developed to calculate a series of statistics in molecular population genetics for both small- and large-scale DNA data, there is no efficient and easy-to-use toolkit available yet for exclusively focusing on the steps of mathematical calculation. Here, we present PopSc, a bioinformatic toolkit for calculating 45 basic statistics in molecular population genetics, which could be categorized into three classes, including (i) genetic diversity of DNA sequences, (ii) statistical tests for neutral evolution, and (iii) measures of genetic differentiation among populations...
2016: PloS One
Leila Sabrina Ullmann, Ramiro das Neves Dias-Neto, Didier Quevedo Cagnini, Ricardo Seiti Yamatogi, Jose Paes Oliveira-Filho, Viviane Nemer, Rodrigo Hidalgo Friciello Teixeira, Alexander Welker Biondo, João Pessoa Araújo
BACKGROUND: Mycobacterium is an important zoonotic agent with companion, livestock and wildlife animals reportedly playing a role as reservoirs. Although its association with reptiles has been described, the disease cycle remains to be fully established, particularly in snakes. Accordingly, this study aimed to report the occurrence of mycobacteriosis with clinical pneumonia in one exotic python snake (Python molurus) and one native green snake (Philodryas olfersii) from the Sorocaba Zoo, São Paulo state, Brazil...
2016: Journal of Venomous Animals and Toxins Including Tropical Diseases
Kristopher J L Irizarry, Randall L Bryden
Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes...
2016: Advances in Bioinformatics
Ilias Georgakopoulos-Soares, Naman Jain, Jesse M Gray, Martin Hemberg
MOTIVATION: With the rapid advances in DNA synthesis and sequencing technologies and the continuing decline in the associated costs, high-throughput experiments can be performed to investigate the regulatory role of thousands of oligonucleotide sequences simultaneously. Nevertheless, designing high-throughput reporter assay experiments such as massively parallel reporter assays (MPRAs) and similar methods remains challenging. RESULTS: We introduce MPRAnator, a set of tools that facilitate rapid design of MPRA experiments...
September 6, 2016: Bioinformatics
Olga S Voitenko, Andi Dhroso, Anna Feldmann, Dmitry Korkin, Olga V Kalinina
MOTIVATION: Due to their high genomic variability, RNA viruses and retroviruses present a unique opportunity for detailed study of molecular evolution. Lentiviruses, with HIV being a notable example, are one of the best studied viral groups: hundreds of thousands of sequences are available together with experimentally resolved three-dimensional structures for most viral proteins. In this work, we use these data to study specific patterns of evolution of the viral proteins, and their relationship to protein interactions and immunogenicity...
September 1, 2016: Bioinformatics
William Poole, David L Gibbs, Ilya Shmulevich, Brady Bernard, Theo A Knijnenburg
MOTIVATION: Combining P-values from multiple statistical tests is a common exercise in bioinformatics. However, this procedure is non-trivial for dependent P-values. Here, we discuss an empirical adaptation of Brown's method (an extension of Fisher's method) for combining dependent P-values which is appropriate for the large and correlated datasets found in high-throughput biology. RESULTS: We show that the Empirical Brown's method (EBM) outperforms Fisher's method as well as alternative approaches for combining dependent P-values using both noisy simulated data and gene expression data from The Cancer Genome Atlas...
September 1, 2016: Bioinformatics
Yvette Temate-Tiagueu, Sahar Al Seesi, Meril Mathew, Igor Mandric, Alex Rodriguez, Kayla Bean, Qiong Cheng, Olga Glebova, Ion Măndoiu, Nicole B Lopanik, Alexander Zelikovsky
BACKGROUND: Assessing pathway activity levels is a plausible way to quantify metabolic differences between various conditions. This is usually inferred from microarray expression data. Wide availability of NGS technology has triggered a demand for bioinformatics tools capable of analyzing pathway activity directly from RNA-Seq data. In this paper we introduce XPathway, a set of tools that compares pathway activity analyzing mapping of contigs assembled from RNA-Seq reads to KEGG pathways...
2016: BMC Genomics
Sébastien Buchoux
: When studying biological membranes, Molecular Dynamics (MD) simulations reveal to be quite complementary to experimental techniques. Because the simulated systems keep increasing both in size and complexity, the analysis of MD trajectories need to be computationally efficient while being robust enough to perform analysis on membranes that may be curved or deformed due to their size and/or protein-lipid interactions. This work presents a new software named FATSLiM ('Fast Analysis Toolbox for Simulations of Lipid Membranes') that can extract physical properties from MD simulations of membranes (with or without interacting proteins)...
August 29, 2016: Bioinformatics
Eisuke Hayakawa, Yoshinori Fujimura, Daisuke Miura
: Mass spectrometry imaging (MSI) visualizes the simultaneous lateral distribution of multiple compounds on sample surface. However, it is still difficult to visualize biological indices such as energy charge index from multiple compounds because of the lack of publicly available tools. Here we present MSIdV, a visualization tool for biological indices calculated from mass spectrometry imaging data, which can effectively scan a series of mass spectra and process, calculate and visualize user-defined index measures accurately with a number of signal processing features...
August 19, 2016: Bioinformatics
Niels W Hanson, Kishori M Konwar, Steven J Hallam
MOTIVATION: A perennial problem in the analysis of environmental sequence information is the assignment of reads or assembled sequences, e.g. contigs or scaffolds, to discrete taxonomic bins. In the absence of reference genomes for most environmental microorganisms, the use of intrinsic nucleotide patterns and phylogenetic anchors can improve assembly-dependent binning needed for more accurate taxonomic and functional annotation in communities of microorganisms, and assist in identifying mobile genetic elements or lateral gene transfer events...
December 1, 2016: Bioinformatics
Ángel Goñi-Moreno, Juhyun Kim, Víctor de Lorenzo
Visualization of the intracellular constituents of individual bacteria while performing as live biocatalysts is in principle doable through more or less sophisticated fluorescence microscopy. Unfortunately, rigorous quantitation of the wealth of data embodied in the resulting images requires bioinformatic tools that are not widely extended within the community-let alone that they are often subject to licensing that impedes software reuse. In this context we have developed CellShape, a user-friendly platform for image analysis with subpixel precision and double-threshold segmentation system for quantification of fluorescent signals stemming from single-cells...
August 5, 2016: Biotechnology Journal
Daniel A Cuevas, Janaka Edirisinghe, Chris S Henry, Ross Overbeek, Taylor G O'Connell, Robert A Edwards
Microbiological studies are increasingly relying on in silico methods to perform exploration and rapid analysis of genomic data, and functional genomics studies are supplemented by the new perspectives that genome-scale metabolic models offer. A mathematical model consisting of a microbe's entire metabolic map can be rapidly determined from whole-genome sequencing and annotating the genomic material encoded in its DNA. Flux-balance analysis (FBA), a linear programming technique that uses metabolic models to predict the phenotypic responses imposed by environmental elements and factors, is the leading method to simulate and manipulate cellular growth in silico...
2016: Frontiers in Microbiology
Yuanhua Huang, Guido Sanguinetti
MOTIVATION: Isoform quantification is an important goal of RNA-seq experiments, yet it remains problematic for genes with low expression or several isoforms. These difficulties may in principle be ameliorated by exploiting correlated experimental designs, such as time series or dosage response experiments. Time series RNA-seq experiments, in particular, are becoming increasingly popular, yet there are no methods that explicitly leverage the experimental design to improve isoform quantification...
October 1, 2016: Bioinformatics
Kai Kruse, Clemens B Hug, Benjamín Hernández-Rodríguez, Juan M Vaquerizas
: Eukaryotic genomes are hierarchically organized into topologically associating domains (TADs). The computational identification of these domains and their associated properties critically depends on the choice of suitable parameters of TAD-calling algorithms. To reduce the element of trial-and-error in parameter selection, we have developed TADtool: an interactive plot to find robust TAD-calling parameters with immediate visual feedback. TADtool allows the direct export of TADs called with a chosen set of parameters for two of the most common TAD calling algorithms: directionality and insulation index...
June 17, 2016: Bioinformatics
Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller
MOTIVATION: Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis. RESULTS: We present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified...
October 1, 2016: Bioinformatics
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