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https://www.readbyqxmd.com/read/28498885/proximate-a-database-of-mutant-protein-protein-complex-thermodynamics-and-kinetics
#1
Sherlyn Jemimah, K Yugandhar, M Michael Gromiha
Summary: We have developed PROXiMATE, a database of thermodynamic data for more than 6000 missense mutations in 174 heterodimeric protein-protein complexes, supplemented with interaction network data from STRING database, solvent accessibility, sequence, structural and functional information, experimental conditions and literature information. Additional features include complex structure visualization, search and display options, download options and a provision for users to upload their data...
May 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28472345/stopgap-a-database-for-systematic-target-opportunity-assessment-by-genetic-association-predictions
#2
Judong Shen, Kijoung Song, Andrew Slater, Enrico Ferrero, Matthew R Nelson
Summary: We developed the STOPGAP (Systematic Target OPportunity assessment by Genetic Association Predictions) database, an extensive catalog of human genetic associations mapped to effector gene candidates. STOPGAP draws on a variety of publicly available GWAS associations, linkage disequilibrium (LD) measures, functional genomic and variant annotation sources. Algorithms were developed to merge the association data, partition associations into non-overlapping LD clusters, map variants to genes and produce a variant-to-gene score used to rank the relative confidence among potential effector genes...
May 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28472272/modlamp-python-for-antimicrobial-peptides
#3
Alex T Müller, Gisela Gabernet, Jan A Hiss, Gisbert Schneider
Summary: We have implemented the lecular esign aboratory's nti icrobial eptides package ( ), a Python-based software package for the design, classification, and visual representation of peptide data. modlAMP offers functions for molecular descriptor calculation and the retrieval of amino acid sequences from public or local sequence databases, and provides instant access to precompiled data sets for machine learning. The package also contains methods for the analysis and representation of circular dichroism spectra...
May 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28472230/omsim-a-simulator-for-optical-map-data
#4
Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
Motivation: The Bionano Genomics platform allows for the optical detection of short sequence patterns in very long DNA molecules (up to 2.5 Mbp). Molecules with overlapping patterns can be assembled to generate a consensus optical map of the entire genome. In turn, these optical maps can be used to validateor improve de novo genome assembly projects or to detect large-scale structural variation in genomes. Simulated optical map data can assist in the development and benchmarking of tools that operate on thosedata, such as alignment and assembly software...
May 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453684/mappi-dat-data-management-and-analysis-for-protein-protein-interaction-data-from-the-high-throughput-mappit-cell-microarray-platform
#5
Surya Gupta, Veronic De Puysseleyr, José Van der Heyden, Davy Maddelein, Irma Lemmens, Sam Lievens, Sven Degroeve, Jan Tavernier, Lennart Martens
Summary: Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453672/primerize-2d-automated-primer-design-for-rna-multidimensional-chemical-mapping
#6
Siqi Tian, Rhiju Das
Summary: Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449031/rnablueprint-flexible-multiple-target-nucleic-acid-sequence-design
#7
Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L Hofacker, Sven Findeiß
Motivation: Realizing the value of synthetic biology in biotechnology and medicine requires the design of molecules with specialized functions. Due to its close structure to function relationship, and the availability of good structure prediction methods and energy models, RNA is perfectly suited to be synthetically engineered with predefined properties. However, currently available RNA design tools cannot be easily adapted to accommodate new design specifications. Furthermore, complicated sampling and optimization methods are often developed to suit a specific RNA design goal, adding to their inflexibility...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28431529/hirbin-high-resolution-identification-of-differentially-abundant-functions-in-metagenomes
#8
Tobias Österlund, Viktor Jonsson, Erik Kristiansson
BACKGROUND: Gene-centric analysis of metagenomics data provides information about the biochemical functions present in a microbiome under a certain condition. The ability to identify significant differences in functions between metagenomes is dependent on accurate classification and quantification of the sequence reads (binning). However, biological effects acting on specific functions may be overlooked if the classes are too general. METHODS: Here we introduce High-Resolution Binning (HirBin), a new method for gene-centric analysis of metagenomes...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28409116/prepare_taxa_charts-py-a-python-program-to-automate-generation-of-publication-ready-taxonomic-pie-chart-images-from-qiime
#9
Vijay Lakhujani, Chandan Badapanda
QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28403240/snovault-and-encoded-a-novel-object-based-storage-system-and-applications-to-encode-metadata
#10
Benjamin C Hitz, Laurence D Rowe, Nikhil R Podduturi, David I Glick, Ulugbek K Baymuradov, Venkat S Malladi, Esther T Chan, Jean M Davidson, Idan Gabdank, Aditi K Narayana, Kathrina C Onate, Jason Hilton, Marcus C Ho, Brian T Lee, Stuart R Miyasato, Timothy R Dreszer, Cricket A Sloan, J Seth Strattan, Forrest Y Tanaka, Eurie L Hong, J Michael Cherry
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage, unified processing, and distribution to community resources and the scientific community...
2017: PloS One
https://www.readbyqxmd.com/read/28402395/mzml2isa-nmrml2isa-generating-enriched-isa-tab-metadata-files-from-metabolomics-xml-data
#11
Martin Larralde, Thomas N Lawson, Ralf J M Weber, Pablo Moreno, Kenneth Haug, Philippe Rocca-Serra, Mark R Viant, Christoph Steinbeck, Reza M Salek
Summary: Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files...
April 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28398502/pygold-a-python-based-api-for-docking-based-virtual-screening-workflow-generation
#12
Hitesh Patel, Tobias Brinkjost, Oliver Koch
Motivation: Molecular docking is one of the successful approaches in structure based discovery and development of bioactive molecules in chemical biology and medicinal chemistry. Due to the huge amount of computational time that is still required, docking is often the last step in a virtual screening approach. Such screenings are set as workflows spanned over many steps, each aiming at different filtering task. These workflows can be automatized in large parts using python based toolkits except for docking using the docking software GOLD...
April 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28388874/pgltools-a-genomic-arithmetic-tool-suite-for-manipulation-of-hi-c-peak-and-other-chromatin-interaction-data
#13
William W Greenwald, He Li, Erin N Smith, Paola Benaglio, Naoki Nariai, Kelly A Frazer
BACKGROUND: Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from "genomic interaction" studies...
April 7, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28379466/mackinac-a-bridge-between-modelseed-and-cobrapy-to-generate-and-analyze-genome-scale-metabolic-models
#14
Michael Mundy, Helena Mendes-Soares, Nicholas Chia
Summary: Reconstructing and analyzing a large number of genome-scale metabolic models is a fundamental part of the integrated study of microbial communities; however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Here we describe Mackinac, a Python package that combines ModelSEED's ability to automatically reconstruct metabolic models with COBRApy's advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms...
August 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28369284/spresso-an-ultrafast-compound-pre-screening-method-based-on-compound-decomposition
#15
Keisuke Yanagisawa, Shunta Komine, Shogo D Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama
Motivation: Recently, the number of available protein tertiary structures and compounds has increased. However, structure-based virtual screening is computationally expensive owing to docking simulations. Thus, methods that filter out obviously unnecessary compounds prior to computationally expensive docking simulations have been proposed. However, the calculation speed of these methods is not fast enough to evaluate ≥ 10 million compounds. Results: In this article, we propose a novel, docking-based pre-screening protocol named Spresso (Speedy PRE-Screening method with Segmented cOmpounds)...
March 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28369168/conkit-a-python-interface-to-contact-predictions
#16
Felix Simkovic, Jens M H Thomas, Daniel J Rigden
Summary: Recent advances in protein residue contact prediction algorithms have led to the emergence of many new methods and a variety of file formats. We present ConKit , an open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions. Availability and implementation: ConKit is available via the Python Package Index. The documentation can be found at http://www...
March 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28369166/cpipe-a-comprehensive-computational-platform-for-sequence-and-structure-based-analyses-of-cysteine-residues
#17
Inanc Soylu, Stefano M Marino
Summary: Due to their chemical plasticity, Cysteine residues (Cys) can serve many different functions. Identification and classification of reactive Cys isn't a trivial job: currently, no available tool exists for an all-round, comprehensive (inclusive of all different functional types) analysis of Cys; herein we present a computational platform called Cp i pe, dedicated to this task: it implements state-of-the art protocols, elaborating and displaying a wealth of information, sufficiently orthogonal to allow a thorough evaluation of all major aspects of Cys reactivity...
March 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334360/hla-ma-simple-yet-powerful-matching-of-samples-using-hla-typing-results
#18
Clemens Messerschmidt, Manuel Holtgrewe, Dieter Beule
Summary: We propose the simple method HLA-MA for consistency checking in pipelines operating on human HTS data. The method is based on the HLA typing result of the state-of-the-art method OptiType. Provided that there is sufficient coverage of the HLA loci, comparing HLA types allows for simple, fast, and robust matching of samples from whole genome, exome, and RNA-seq data. Our approach uses information from small but genetically highly variable regions and thus complements approaches that rely on genome or exon-wide variant profiles...
March 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334266/phenopolis-an-open-platform-for-harmonization-and-analysis-of-genetic-and-phenotypic-data
#19
Nikolas Pontikos, Jing Yu, Ismail Moghul, Lucy Withington, Fiona Blanco-Kelly, Tom Vulliamy, Tsz Lun Wong, Cian Murphy, Valentina Cipriani, Alessia Fiorentino, Gavin Arno, Daniel Greene, Julius Ob Jacobsen, Tristan Clark, David S Gregory, Andrea Nemeth, Stephanie Halford, Chris F Inglehearn, Susan Downes, Graeme C Black, Andrew R Webster, Alison J Hardcastle, Vincent Plagnol
Summary: Phenopolis is an open-source web server providing an intuitive interface to genetic and phenotypic databases. It integrates analysis tools such as variant filtering and gene prioritisation based on phenotype. The Phenopolis platform will accelerate clinical diagnosis, gene discovery and encourage wider adoption of the Human Phenotype Ontology in the study of rare genetic diseases. Availability and Implementation: A demo of the website is available at https://phenopolis...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334194/swga-a-primer-design-toolkit-for-selective-whole-genome-amplification
#20
Erik L Clarke, Sesh A Sundararaman, Stephanie N Seifert, Frederic D Bushman, Beatrice H Hahn, Dustin Brisson
Motivation: Population genomic analyses are often hindered by difficulties in obtaining sufficient numbers of genomes for analysis by DNA sequencing. Selective whole-genome amplification (SWGA) provides an efficient approach to amplify microbial genomes from complex backgrounds for sequence acquisition. However, the process of designing sets of primers for this method has many degrees of freedom and would benefit from an automated process to evaluate the vast number of potential primer sets...
February 27, 2017: Bioinformatics
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