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https://www.readbyqxmd.com/read/28093409/deuterater-a-tool-for-quantifying-peptide-isotope-precision-and-kinetic-proteomics
#1
Bradley C Naylor, Michael T Porter, Elise Wilson, Adam Herring, Spencer Lofthouse, Austin Hannemann, Stephen R Piccolo, Alan L Rockwood, John C Price
MOTIVATION: Using mass spectrometry to measure the concentration and turnover of the individual proteins in a proteome, enables the calculation of individual synthesis and degradation rates for each protein. Software to analyze concentration is readily available, but software to analyze turnover is lacking. Data analysis workflows typically don't access the full breadth of information about instrument precision and accuracy that is present in each peptide isotopic envelope measurement...
January 16, 2017: Bioinformatics
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/28062450/the-structural-bioinformatics-library-modeling-in-biomolecular-science-and-beyond
#3
Frédéric Cazals, Tom Dreyfus
MOTIVATION: Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library (SBL, http://sbl.inria.fr), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28011770/simulation-based-estimation-of-branching-models-for-ltr-retrotransposons
#4
Serge Moulin, Nicolas Seux, Stéphane Chrétien, Christophe Guyeux, Emmanuelle Lerat
MOTIVATION: LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. RESULTS: Various functions have been implemented in order to simulate their spread and visualization tools are proposed...
October 6, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27993786/defcom-analysis-and-modeling-of-transcription-factor-binding-sites-using-a-motif-centric-genomic-footprinter
#5
Bryan Quach, Terrence S Furey
MOTIVATION: Identifying the locations of transcription factor binding sites is critical for understanding how gene transcription is regulated across different cell types and conditions. Chromatin accessibility experiments such as DNaseI sequencing (DNase-seq) and Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) produce genome-wide data that include distinct "footprint" patterns at binding sites. Nearly all existing computational methods to detect footprints from these data assume that footprint signals are highly homogeneous across footprint sites...
December 19, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27990269/disambiguate-an-open-source-application-for-disambiguating-two-species-in-next-generation-sequencing-data-from-grafted-samples
#6
Miika J Ahdesmäki, Simon R Gray, Justin H Johnson, Zhongwu Lai
Grafting of cell lines and primary tumours is a crucial step in the drug development process between cell line studies and clinical trials. Disambiguate is a program for computationally separating the sequencing reads of two species derived from grafted samples. Disambiguate operates on alignments to the two species and separates the components at very high sensitivity and specificity as illustrated in artificially mixed human-mouse samples. This allows for maximum recovery of data from target tumours for more accurate variant calling and gene expression quantification...
2016: F1000Research
https://www.readbyqxmd.com/read/27797777/integrate-neo-a-pipeline-for-personalized-gene-fusion-neoantigen-discovery
#7
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 AND IMPLEMENTATION: INTEGRATE-Neo is implemented in C ++ and Python...
October 24, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27797766/ymap-an-automated-method-to-map-yeast-variants-to-protein-modifications-and-functional-regions
#8
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
https://www.readbyqxmd.com/read/27797763/rabifier2-an-improved-bioinformatic-classifier-of-rab-gtpases
#9
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
https://www.readbyqxmd.com/read/27794557/fractbias-a-graphical-tool-for-assessing-fractionation-bias-following-polyploidy
#10
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
https://www.readbyqxmd.com/read/27793083/mevolib-v1-0-the-first-molecular-evolution-library-for-python
#11
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
https://www.readbyqxmd.com/read/27792763/popsc-computing-toolkit-for-basic-statistics-of-molecular-population-genetics-simultaneously-implemented-in-web-based-calculator-python-and-r
#12
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
https://www.readbyqxmd.com/read/27777582/mycobacterium-genavense-infection-in-two-species-of-captive-snakes
#13
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
https://www.readbyqxmd.com/read/27698666/in-silico-analysis-of-gene-expression-network-components-underlying-pigmentation-phenotypes-in-the-python-identified-evolutionarily-conserved-clusters-of-transcription-factor-binding-sites
#14
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
https://www.readbyqxmd.com/read/27605100/mpranator-a-web-based-tool-for-the-design-of-massively-parallel-reporter-assay-experiments
#15
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...
January 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/27587690/patterns-of-amino-acid-conservation-in-human-and-animal-immunodeficiency-viruses
#16
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
https://www.readbyqxmd.com/read/27587659/combining-dependent-p-values-with-an-empirical-adaptation-of-brown-s-method
#17
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
https://www.readbyqxmd.com/read/27585456/inferring-metabolic-pathway-activity-levels-from-rna-seq-data
#18
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
https://www.readbyqxmd.com/read/27578804/fatslim-a-fast-and-robust-software-to-analyze-md-simulations-of-membranes
#19
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)...
January 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/27542771/msidv-a-versatile-tool-to-visualize-biological-indices-from-mass-spectrometry-imaging-data
#20
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...
December 15, 2016: Bioinformatics
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