PoseFilter: a PyMOL plugin for filtering and analyzing small molecule docking in symmetric binding sites

2021 ◽  
Author(s):  
Justine C Williams ◽  
Subha Kalyaanamoorthy
Keyword(s):  
Graphical User Interface ◽  
Binding Sites ◽  
Supplementary Information ◽  
Command Line ◽  
Mean Square ◽  
Supplementary Data ◽  
Oligomeric Protein ◽  
Molecule Docking ◽  
Interaction Fingerprints ◽  
Pymol Plugin

Abstract Summary ‘PoseFilter’ is a PyMOL plugin that assists in analyses and filtering of docked poses. PoseFilter enables automatic detection of symmetric poses from docking outputs and can be accessed using both graphical user interface and command-line options within the PyMOL program. Two methods of analyses, root mean square deviations and interaction fingerprints, are available from this plugin. The capabilities of the plugin are demonstrated using docking outputs from different oligomeric protein-ligand complexes. Availability and implementation The plugin can be downloaded from the GitHub page, https://github.com/skalyaanamoorthy/PoseFilter. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Audit logs to enforce document integrity in Skyline and Panorama

2020 ◽  
Vol 36 (15) ◽  
pp. 4366-4368
Author(s):  
Tobias Rohde ◽  
Rita Chupalov ◽  
Nicholas Shulman ◽  
Vagisha Sharma ◽  
Josh Eckels ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Quantitative Data ◽  
Supplementary Information ◽  
Command Line ◽  
Supplementary Data ◽  
Spectrometry Method ◽  
Quantitative Data Analysis ◽  
User Actions ◽  
Web Repository

Abstract Summary Skyline is a Windows application for targeted mass spectrometry method creation and quantitative data analysis. Like most graphical user interface (GUI) tools, it has a complex user interface with many ways for users to edit their files which makes the task of logging user actions challenging and is the reason why audit logging of every change is not common in GUI tools. We present an object comparison-based approach to audit logging for Skyline that is extensible to other GUI tools. The new audit logging system keeps track of all document modifications made through the GUI or the command line and displays them in an interactive grid. The audit log can also be uploaded and viewed in Panorama, a web repository for Skyline documents that can be configured to only accept documents with a valid audit log, based on embedded hashes to protect log integrity. This makes workflows involving Skyline and Panorama more reproducible. Availability and implementation Skyline is freely available at https://skyline.ms. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data

2020 ◽  
Vol 36 (10) ◽  
pp. 3263-3265 ◽  
Author(s):  
Lucas Czech ◽  
Pierre Barbera ◽  
Alexandros Stamatakis
Keyword(s):  
Phylogenetic Trees ◽  
Supplementary Information ◽  
Command Line ◽  
Supplementary Data ◽  
Computationally Efficient ◽  
Data Types ◽  
Low Level ◽  
Phylogenetic Placement ◽  
Command Line Tool ◽  
High Level

Abstract Summary We present genesis, a library for working with phylogenetic data, and gappa, an accompanying command-line tool for conducting typical analyses on such data. The tools target phylogenetic trees and phylogenetic placements, sequences, taxonomies and other relevant data types, offer high-level simplicity as well as low-level customizability, and are computationally efficient, well-tested and field-proven. Availability and implementation Both genesis and gappa are written in modern C++11, and are freely available under GPLv3 at http://github.com/lczech/genesis and http://github.com/lczech/gappa. Supplementary information Supplementary data are available at Bioinformatics online.

Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants

2019 ◽  
Vol 35 (21) ◽  
pp. 4405-4407 ◽  
Author(s):  
Steven Monger ◽  
Michael Troup ◽  
Eddie Ip ◽  
Sally L Dunwoodie ◽  
Eleni Giannoulatou
Keyword(s):  
Supplementary Information ◽  
Command Line ◽  
Supplementary Data ◽  
In Silico Prediction ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Prediction Tools ◽  
Motif Prediction ◽  
Command Line Tool ◽  
Genome Scale

Abstract Motivation In silico prediction tools are essential for identifying variants which create or disrupt cis-splicing motifs. However, there are limited options for genome-scale discovery of splice-altering variants. Results We have developed Spliceogen, a highly scalable pipeline integrating predictions from some of the individually best performing models for splice motif prediction: MaxEntScan, GeneSplicer, ESRseq and Branchpointer. Availability and implementation Spliceogen is available as a command line tool which accepts VCF/BED inputs and handles both single nucleotide variants (SNVs) and indels (https://github.com/VCCRI/Spliceogen). SNV databases with prediction scores are also available, covering all possible SNVs at all genomic positions within all Gencode-annotated multi-exon transcripts. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals aCLImatise: automated generation of tool definitions for bioinformatics workflows

2020 ◽  
Author(s):  
Michael Milton ◽  
Natalie Thorne
Keyword(s):  
Source Code ◽  
Supplementary Information ◽  
Command Line ◽  
Supplementary Data ◽  
Automated Generation ◽  
Base Camp ◽  
Python Package ◽  
Bioinformatics Workflow ◽  
Bioinformatics Workflows

Abstract Summary aCLImatise is a utility for automatically generating tool definitions compatible with bioinformatics workflow languages, by parsing command-line help output. aCLImatise also has an associated database called the aCLImatise Base Camp, which provides thousands of pre-computed tool definitions. Availability and implementation The latest aCLImatise source code is available within a GitHub organisation, under the GPL-3.0 license: https://github.com/aCLImatise. In particular, documentation for the aCLImatise Python package is available at https://aclimatise.github.io/CliHelpParser/, and the aCLImatise Base Camp is available at https://aclimatise.github.io/BaseCamp/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Visualization of circular RNAs and their internal splicing events from transcriptomic data

2020 ◽  
Vol 36 (9) ◽  
pp. 2934-2935 ◽  
Author(s):  
Yi Zheng ◽  
Fangqing Zhao
Keyword(s):  
Supplementary Information ◽  
Circular Rnas ◽  
Visualization Tool ◽  
Command Line ◽  
Supplementary Data ◽  
Transcriptomic Data ◽  
Command Line Tool ◽  
Transcriptome Comparison ◽  
Multiple Samples ◽  
Splicing Patterns

Abstract Summary Circular RNAs (circRNAs) are proved to have unique compositions and splicing events distinct from canonical mRNAs. However, there is no visualization tool designed for the exploration of complex splicing patterns in circRNA transcriptomes. Here, we present CIRI-vis, a Java command-line tool for quantifying and visualizing circRNAs by integrating the alignments and junctions of circular transcripts. CIRI-vis can be applied to visualize the internal structure and isoform abundance of circRNAs and perform circRNA transcriptome comparison across multiple samples. Availability and implementation https://sourceforge.net/projects/ciri/files/CIRI-vis. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos

2019 ◽  
Author(s):  
A Trullo ◽  
J Dufourt ◽  
M Lagha
Keyword(s):  
Graphical User Interface ◽  
Transcriptional Activation ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Automatic Image Analysis ◽  
Lineage Tree ◽  
Automatic Software ◽  
Integrated Software ◽  
Lineage Tracking ◽  
User Friendly

Abstract Motivation During development, progenitor cells undergo multiple rounds of cellular divisions during which transcriptional programs must be faithfully propagated. Investigating the timing of transcriptional activation, which is a highly stochastic phenomenon, requires the analysis of large amounts of data. In order to perform automatic image analysis of transcriptional activation, we developed a software that segments and tracks both small and large objects, leading the user from raw data up to the results in their final form. Results MitoTrack is a user-friendly open-access integrated software that performs the specific dual task of reporting the precise timing of transcriptional activation while keeping lineage tree history for each nucleus of a living developing embryo. The software works automatically but provides the possibility to easily supervise, correct and validate each step. Availability and implementation MitoTrack is an open source Python software, embedded within a graphical user interface (download here). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Knot_pull—python package for biopolymer smoothing and knot detection

2019 ◽  
Author(s):  
Aleksandra I Jarmolinska ◽  
Anna Gambin ◽  
Joanna I Sulkowska
Keyword(s):  
Learning Curve ◽  
Source Code ◽  
Supplementary Information ◽  
Command Line ◽  
Supplementary Data ◽  
Steep Learning Curve ◽  
Independent Source ◽  
Python Package

Abstract Summary The biggest hurdle in studying topology in biopolymers is the steep learning curve for actually seeing the knots in structure visualization. Knot_pull is a command line utility designed to simplify this process—it presents the user with a smoothing trajectory for provided structures (any number and length of protein, RNA or chromatin chains in PDB, CIF or XYZ format), and calculates the knot type (including presence of any links, and slipknots when a subchain is specified). Availability and implementation Knot_pull works under Python >=2.7 and is system independent. Source code and documentation are available at http://github.com/dzarmola/knot_pull under GNU GPL license and include also a wrapper script for PyMOL for easier visualization. Examples of smoothing trajectories can be found at: https://www.youtube.com/watch?v=IzSGDfc1vAY. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Phylonium: fast estimation of evolutionary distances from large samples of similar genomes

2019 ◽  
Vol 36 (7) ◽  
pp. 2040-2046 ◽  
Author(s):  
Fabian Klötzl ◽  
Bernhard Haubold
Keyword(s):  
Disease Outbreaks ◽  
Supplementary Information ◽  
Whole Genome ◽  
Command Line ◽  
Supplementary Data ◽  
Large Samples ◽  
Fast Estimation ◽  
Unix Command ◽  
Similar Accuracy ◽  
Single Sequence

Abstract Motivation Tracking disease outbreaks by whole-genome sequencing leads to the collection of large samples of closely related sequences. Five years ago, we published a method to accurately compute all pairwise distances for such samples by indexing each sequence. Since indexing is slow, we now ask whether it is possible to achieve similar accuracy when indexing only a single sequence. Results We have implemented this idea in the program phylonium and show that it is as accurate as its predecessor and roughly 100 times faster when applied to all 2678 Escherichia coli genomes contained in ENSEMBL. One of the best published programs for rapidly computing pairwise distances, mash, analyzes the same dataset four times faster but, with default settings, it is less accurate than phylonium. Availability and implementation Phylonium runs under the UNIX command line; its C++ sources and documentation are available from github.com/evolbioinf/phylonium. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals pyGenomeTracks: reproducible plots for multivariate genomic data sets

2020 ◽  
Author(s):  
Lucille Lopez-Delisle ◽  
Leily Rabbani ◽  
Joachim Wolff ◽  
Vivek Bhardwaj ◽  
Rolf Backofen ◽  
...  
Keyword(s):  
Genomic Data ◽  
Supplementary Information ◽  
Data Sets ◽  
Command Line ◽  
Graphical Interface ◽  
Supplementary Data ◽  
Considerable Effort ◽  
Vector Graphic ◽  
Graphic Software

Abstract Motivation Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures requires considerable effort. This is usually done by hand or by using a vector graphic software. Results pyGenomeTracks (PGT) is a modular plotting tool that easily combines multiple tracks. It enables a reproducible and standardized generation of highly customizable and publication ready images. Availability PGT is available through a graphical interface on https://usegalaxy.eu and through the command line. It is provided on conda via the bioconda channel, on pip and it is openly developed on github: https://github.com/deeptools/pyGenomeTracks. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets

2018 ◽  
Vol 35 (13) ◽  
pp. 2318-2319 ◽  
Author(s):  
Matthew D Czajkowski ◽  
Daniel P Vance ◽  
Steven A Frese ◽  
Giorgio Casaburi
Keyword(s):  
User Interface ◽  
Human Genome ◽  
Graphical User Interface ◽  
Supplementary Information ◽  
Metagenomic Sequencing ◽  
Command Line ◽  
Shotgun Metagenomic Sequencing ◽  
Human Genomic ◽  
Quality Filtering ◽  
Analytical Time

Abstract Summary The removal of human genomic reads from shotgun metagenomic sequencing is a critical step in protecting subject privacy. Freely available tools addressing this issue require advanced programing knowledge or are limited by analytical time and data load due to their server-based nature. Here, we compared the most cited tools for host-DNA removal using synthetic and real metagenomic datasets. Then, we integrated the most efficient pipeline in a graphical user interface to make these tools available without command line use. This interface, GenCoF, rapidly removes human genome contaminants from metagenomic datasets. Additionally, the tool offers quality-filtering, data reduction and interactive modification of any parameter in order to customize the analysis. GenCoF offers both quality and host-associated filtering in a non-commercial, freely available tool in a local, interactive and easy-to-use interface. Availability and implementation GenCoF is freely available (under a GPL license) for Mac OS and Linux at https://github.com/MattCzajkowski/GenCoF. Supplementary information Supplementary data are available at Bioinformatics online.

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