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https://www.readbyqxmd.com/read/28886064/sexcmd-development-and-validation-of-sex-marker-sequences-for-whole-exome-genome-and-rna-sequencing
#1
Seongmun Jeong, Jiwoong Kim, Won Park, Hongmin Jeon, Namshin Kim
Over the last decade, a large number of nucleotide sequences have been generated by next-generation sequencing technologies and deposited to public databases. However, most of these datasets do not specify the sex of individuals sampled because researchers typically ignore or hide this information. Male and female genomes in many species have distinctive sex chromosomes, XX/XY and ZW/ZZ, and expression levels of many sex-related genes differ between the sexes. Herein, we describe how to develop sex marker sequences from syntenic regions of sex chromosomes and use them to quickly identify the sex of individuals being analyzed...
2017: PloS One
https://www.readbyqxmd.com/read/28882003/minimds-3d-structural-inference-from-high-resolution-hi-c-data
#2
Lila Rieber, Shaun Mahony
Motivation: Recent experiments have provided Hi-C data at resolution as high as 1 kbp. However, 3D structural inference from high-resolution Hi-C datasets is often computationally unfeasible using existing methods. Results: We have developed miniMDS, an approximation of multidimensional scaling (MDS) that partitions a Hi-C dataset, performs high-resolution MDS separately on each partition, and then reassembles the partitions using low-resolution MDS. miniMDS is faster, more accurate, and uses less memory than existing methods for inferring the human genome at high resolution (10 kbp)...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28666322/svm-dependent-pairwise-hmm-an-application-to-protein-pairwise-alignments
#3
Gabriele Orlando, Daniele Raimondi, Taushif Khan, Tom Lenaerts, Wim Vranken
Motivation: Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions...
June 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28666314/gpu-powered-model-analysis-with-pysb-cupsoda
#4
Leonard A Harris, Marco S Nobile, James C Pino, Alexander L R Lubbock, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga, Carlos F Lopez
Summary: A major barrier to the practical utilization of large, complex models of biochemical systems is the lack of open-source computational tools to evaluate model behaviors over high-dimensional parameter spaces. This is due to the high computational expense of performing thousands to millions of model simulations required for statistical analysis. To address this need, we have implemented a user-friendly interface between cupSODA, a GPU-powered kinetic simulator, and PySB, a Python-based modeling and simulation framework...
June 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28655203/kronos-a-workflow-assembler-for-genome-analytics-and-informatics
#5
M Jafar Taghiyar, Jamie Rosner, Diljot Grewal, Bruno M Grande, Radhouane Aniba, Jasleen Grewal, Paul C Boutros, Ryan D Morin, Ali Bashashati, Sohrab P Shah
Background: The field of next generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into 'best practices' for automated analysis of NGS datasets) still requires significant programming investment and expertise. Results: We present Kronos , a software platform for facilitating the development and execution of modular, auditable and distributable bioinformatics workflows...
June 26, 2017: GigaScience
https://www.readbyqxmd.com/read/28655158/coretracker-accurate-codon-reassignment-prediction-applied-to-mitochondrial-genomes
#6
Noutahi Emmanuel, Calderon Virginie, Blanchette Mathieu, Lang B Franz, El-Mabrouk Nadia
Motivation: Codon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes. These tools can only analyze a single genome at a time and are often not followed by a validation procedure, resulting in a high rate of false positives...
June 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28646877/sbmlmod-a-python-based-web-application-and-web-service-for-efficient-data-integration-and-model-simulation
#7
Sascha Schäuble, Anne-Kristin Stavrum, Mathias Bockwoldt, Pål Puntervoll, Ines Heiland
BACKGROUND: Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting. RESULTS: We present SBMLmod, a Python-based web application and service, that automates integration of high throughput data into SBML models...
June 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28645150/gfapy-a-flexible-and-extensible-software-library-for-handling-sequence-graphs-in-python
#8
Giorgio Gonnella, Stefan Kurtz
Summary: GFA 1 and GFA 2 are recently defined formats for representing sequence graphs, such as assembly, variation or splicing graphs. The formats are adopted by several software tools. Availability and Implementation: GfaPy is available open source at https://github.com/ggonnella/gfapy and installable via pip. Contact: gonnella@zbh.uni-hamburg.de. Supplementary information: Supplementary data are available at Bioinformatics online...
June 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637183/nuclitrack-an-integrated-nuclei-tracking-application
#9
Sam Cooper, Alexis R Barr, Robert Glen, Chris Bakal
Summary: Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently-labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack's interactive, graphical interface makes it significantly more user friendly...
June 20, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633344/pheno4j-a-gene-to-phenotype-graph-database
#10
Sajid Mughal, Ismail Moghul, Jing Yu, Tristan Clark, David S Gregory, Nikolas Pontikos
Summary: Efficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and well phenotyped patients into a graph database to allow fast efficient storage and querying of large volumes of structured genetic and phenotypic data. This abstracts technical problems away and lets researchers focus on the science rather than the implementation...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28630199/genomewide-analysis-of-the-antimicrobial-peptides-in-python-bivittatus-and-characterization-of-cathelicidins-with-potent-antimicrobial-activity-and-low-cytotoxicity
#11
Dayeong Kim, Nagasundarapandian Soundrarajan, Juyeon Lee, Hye-Sun Cho, Minkyeung Choi, Se-Yeoun Cha, Byeongyong Ahn, Hyoim Jeon, Minh Thong Le, Hyuk Song, Jin-Hoi Kim, Chankyu Park
In this study, we sought to identify novel antimicrobial peptides (AMPs) in Python bivittatus through bioinformatic analyses of publicly available genome information and experimental validation. In our analysis of the python genome, we identified 29 AMP-related candidate sequences. Of these, we selected five cathelicidin-like sequences and subjected them to further in silico analyses. The results showed that these sequences likely have antimicrobial activity. The sequences were named Pb-CATH1 to Pb-CATH5 according to their sequence similarity to previously reported snake cathelicidins...
September 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28605539/runbng-a-software-package-for-bionano-genomic-analysis-on-the-command-line
#12
Yuxuan Yuan, Philipp E Bayer, HueyTyng Lee, David Edwards
Summary: We developed runBNG, an open-source software package which wraps BioNano genomic analysis tools into a single script that can be run on the command line. runBNG can complete analyses, including quality control of single molecule maps, optical map de novo assembly, comparisons between different optical maps, super-scaffolding and structural variation detection. Compared to existing software BioNano IrysView and the KSU scripts, the major advantages of runBNG are that the whole pipeline runs on one single platform and it has a high customizability ...
June 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28582565/isambard-an-open-source-computational-environment-for-biomolecular-analysis-modelling-and-design
#13
Christopher W Wood, Jack W Heal, Andrew R Thomson, Gail J Bartlett, Amaurys A Ibarra, R Leo Brady, Richard B Sessions, Derek N Woolfson
Motivation: The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users. Results: Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico ...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28582538/breakpoint-surveyor-a-pipeline-for-structural-variant-visualization
#14
Matthew A Wyczalkowski, Kristine M Wylie, Song Cao, Michael D McLellan, Jennifer Flynn, Mo Huang, Kai Ye, Xian Fan, Ken Chen, Michael C Wendl, Li Ding
Summary: BreakPoint Surveyor (BPS) is a computational pipeline for the discovery, characterization, and visualization of complex genomic rearrangements, such as viral genome integration, in paired-end sequence data. BPS facilitates interpretation of structural variants by merging structural variant breakpoint predictions, gene exon structure, read depth, and RNA-Seq expression into a single comprehensive figure. Availability: Source code and sample data freely available for download at https://github...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28582485/compass-the-completely-arbitrary-sequence-simulator
#15
Andrew Low, Nicolas Rodrigue, Alex Wong
Summary: Simulated sequence alignments are frequently used to test bioinformatics tools, but current sequence simulators are limited to defined state spaces. Here, we present the COMPletely Arbitrary Sequence Simulator (COMPASS), which is able to simulate the evolution of absolutely any discrete state space along a tree, for any form of time-reversible model. Availability and Implementation: COMPASS is implemented in Python 2.7, and is freely available for all platforms with the Supplemetary Information, as well as at http://labs...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28582481/fungap-fungal-genome-annotation-pipeline-using-evidence-based-gene-model-evaluation
#16
Byoungnam Min, Igor V Grigoriev, In-Geol Choi
Motivation: Successful genome analysis depends on the quality of gene prediction. Although fungal genome sequencing and assembly have become trivial, its annotation procedure has not been standardized yet. Results: FunGAP predicts protein-coding genes in a fungal genome assembly. To attain high-quality gene models, this program runs multiple gene predictors, evaluates all predicted genes, and assembles gene models that are highly supported by homology to known sequences...
September 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28575169/md-task-a-software-suite-for-analyzing-molecular-dynamics-trajectories
#17
David K Brown, David L Penkler, Olivier Sheik Amamuddy, Caroline Ross, Ali Rana Atilgan, Canan Atilgan, Özlem Tastan Bishop
Summary: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, a novel software suite that employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories...
September 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28572580/uropa-a-tool-for-universal-robust-peak-annotation
#18
Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso
The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure and accessibility experiments (such as ATAC-seq), but also from other types of predictions that result in genomic ranges. While peak annotation primarily driven by ChiP-seq was extensively explored, many approaches remain simplistic ("most closely located TSS"), rely on fixed pre-built references, or require complex scripting tasks on behalf of the user...
June 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28498885/proximate-a-database-of-mutant-protein-protein-complex-thermodynamics-and-kinetics
#19
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...
September 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28472345/stopgap-a-database-for-systematic-target-opportunity-assessment-by-genetic-association-predictions
#20
Judong Shen, Kijoung Song, Andrew J 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...
September 1, 2017: Bioinformatics
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