scholarly journals quasitools: A Collection of Tools for Viral Quasispecies Analysis

2019 ◽  
Author(s):  
Eric Marinier ◽  
Eric Enns ◽  
Camy Tran ◽  
Matthew Fogel ◽  
Cole Peters ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Distance ◽  
Open Source ◽  
Source Code ◽  
Viral Quasispecies ◽  
Consensus Sequences ◽  
Link Type ◽  
Version 2.0 ◽  
Amino Acid Variants

AbstractSummaryquasitools is a collection of newly-developed, open-source tools for analyzing viral quasispcies data. The application suite includes tools with the ability to create consensus sequences, call nucleotide, codon, and amino acid variants, calculate the complexity of a quasispecies, and measure the genetic distance between two similar quasispecies. These tools may be run independently or in user-created workflows.AvailabilityThe quasitools suite is a freely available application licensed under the Apache License, Version 2.0. The source code, documentation, and file specifications are available at: https://phac-nml.github.io/quasitools/[email protected]

scholarly journals SurfStamp: 3D Printer Compatible Molecular Surface Representation

2020 ◽  
Author(s):  
Toshiyuki Oda
Keyword(s):  
Open Source ◽  
Source Code ◽  
3D Structure ◽  
Three Dimensional ◽  
Molecular Surface ◽  
3D Printer ◽  
3D Object ◽  
Link Type ◽  
Surface Models ◽  
Version 2.0

AbstractSurfStamp is an application that is used to generate textures for surface models of proteins. The textures contain information about surface residues and the information is drawn directly on the 3D object of the models. This approach is more intuitive than the labeling functions that most three-dimensional (3D) structure viewers use to show residue information. Therefore, the use of this application enables researchers, readers, or audiences to easily determine which residues are contributing the surface they are focusing on.AvailabilityThe application is provided under the open-source Apache License Version 2.0 (http://www.apache.org/licenses/LICENSE-2.0). The application and source code are available from https://github.com/yamule/SurfStamp-public/releases.

scholarly journals MaveRegistry: a collaboration platform for multiplexed assays of variant effect

2020 ◽  
Author(s):  
Da Kuang ◽  
Jochen Weile ◽  
Nishka Kishore ◽  
Alan F. Rubin ◽  
Stanley Fields ◽  
...  
Keyword(s):  
Amino Acid ◽  
International Community ◽  
Human Variation ◽  
Single Nucleotide ◽  
Clinical Interpretation ◽  
Link Type ◽  
Variant Effect ◽  
Genomic Regions ◽  
Amino Acid Variants

AbstractSummaryMultiplexed assays of variant effect (MAVEs) are capable of experimentally testing all possible single nucleotide or amino acid variants in selected genomic regions, generating ‘variant effect maps’, which provide biochemical insight and functional evidence to enable more rapid and accurate clinical interpretation of human variation. Because the international community applying MAVE approaches is growing rapidly, we developed the online MaveRegistry platform to catalyze collaboration, reduce redundant efforts, allow stakeholders to nominate targets, and enable tracking and sharing of progress on ongoing MAVE projects.Availability and implementationhttps://[email protected]

scholarly journals Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

2021 ◽  
Author(s):  
Soohyun Lee ◽  
Carl Vitzthum ◽  
Burak H. Alver ◽  
Peter J. Park
Keyword(s):  
Quality Control ◽  
Open Source ◽  
Source Code ◽  
Three Dimensional ◽  
File Format ◽  
Interaction Data ◽  
Text File ◽  
Storage And Retrieval ◽  
Link Type ◽  
Efficient Storage

AbstractSummaryAs the amount of three-dimensional chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix, an open-source C application to index and query Pairs files. Pairix (also available in Python and R) extends the functionalities of Tabix to paired coordinates data. We have also developed PairsQC, a collapsible HTML quality control report generator for Pairs files.AvailabilityThe format specification and source code are available at https://github.com/4dn-dcic/pairix, https://github.com/4dn-dcic/Rpairix and https://github.com/4dn-dcic/[email protected] or [email protected]

scholarly journals MaveRegistry: a collaboration platform for multiplexed assays of variant effect

2021 ◽  
Author(s):  
Da Kuang ◽  
Jochen Weile ◽  
Nishka Kishore ◽  
Maria Nguyen ◽  
Alan F Rubin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Source Code ◽  
International Community ◽  
Human Variation ◽  
Single Nucleotide ◽  
Clinical Interpretation ◽  
Front End ◽  
Variant Effect ◽  
Genomic Regions ◽  
Amino Acid Variants

Abstract Summary Multiplexed assays of variant effect (MAVEs) are capable of experimentally testing all possible single nucleotide or amino acid variants in selected genomic regions, generating ‘variant effect maps’, which provide biochemical insight and functional evidence to enable more rapid and accurate clinical interpretation of human variation. Because the international community applying MAVE approaches is growing rapidly, we developed the online MaveRegistry platform to catalyze collaboration, reduce redundant efforts, allow stakeholders to nominate targets and enable tracking and sharing of progress on ongoing MAVE projects. Availability and implementation MaveRegistry service: https://registry.varianteffect.org. MaveRegistry source code: https://github.com/kvnkuang/maveregistry-front-end.

scholarly journals Matchathon: A guide to student-faculty connections in PhD programs

2020 ◽  
Author(s):  
Haley Amemiya ◽  
Zena Lapp ◽  
Cathy Smith ◽  
Margaret Durdan ◽  
Michelle DiMondo ◽  
...  
Keyword(s):  
Open Source ◽  
Source Code ◽  
Faculty Members ◽  
Retention Rates ◽  
Link Type ◽  
Shiny App ◽  
R Shiny ◽  
Web App ◽  
Phd Programs ◽  
The Web

AbstractRelevant and impactful mentors are essential to a graduate student’s career. Finding mentors can be challenging in umbrella programs with hundreds of faculty members. To foster connections between potential mentors and students with similar research interests, we created a Matchathon event, which has successfully enabled students to find mentors. We developed an easy-to-use R Shiny app (https://github.com/UM-OGPS/matchathon/) to facilitate matching and organizing the event that can be used at any institution. It is our hope that this resource will improve the environment and retention rates for students in the academy.The open source app is publicly available on the web (app: https://UM-OGPS.shinyapps.io/matchathon/; source code: https://github.com/UM-OGPS/matchathon/).

scholarly journals A RESTful API to serve BAM file with OAuth2 compatible authorization

2017 ◽  
Author(s):  
Julien Delafontaine ◽  
Sylvain Pradervand
Keyword(s):  
Open Source ◽  
Source Code ◽  
Variant Calling ◽  
Use Case ◽  
Web Interface ◽  
Sensitive Data ◽  
Link Type ◽  
Restful Service

AbstractSummaryBam-server is an open-source RESTful service to query slices of BAM files securely and manage their user accesses. A typical use case is the visualization of local read alignments in a web interface for variant calling diagnostic, without exposing sensitive data to unauthorized users through the network, and without moving the original - heavy - file. Bam-server follows the standard implementation of a protected resource server in the context of a typical token-based authorization protocol, supporting HMAC- and RSA-hashed signatures from an authorization server of choice.AvailabilityThe source code is available at https://github.com/chuv-ssrc/bam-server-scala, and a complete documentation can be found at http://bam-server-scala.readthedocs.io/en/latest/[email protected]

scholarly journals Edlib: a C/C++ library for fast, exact sequence alignment using edit distance

2016 ◽  
Author(s):  
Martin Šošić ◽  
Mile Šikić
Keyword(s):  
Exact Sequence ◽  
Open Source ◽  
Sequence Alignment ◽  
Test Data ◽  
Edit Distance ◽  
Source Code ◽  
Memory Usage ◽  
Pairwise Sequence Alignment ◽  
Link Type ◽  
Bioinformatics Tools

AbstractWe present Edlib, an open-source C/C++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality, and can also easily handle very large sequences. Being easy to use, flexible, fast and low on memory usage, we expect it to be a cornerstone for many future bioinformatics tools.Source code, installation instructions and test data are freely available for download at https://github.com/Martinsos/edlib, implemented in C/C++ and supported on Linux, MS Windows, and Mac OS.Contact:[email protected]

scholarly journals ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions

2019 ◽  
Author(s):  
Egor Dolzhenko ◽  
Viraj Deshpande ◽  
Felix Schlesinger ◽  
Peter Krusche ◽  
Roman Petrovski ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Broad Class ◽  
Source Code ◽  
Computational Method ◽  
Dna Repeats ◽  
Link Type ◽  
Sequence Graph ◽  
Version 2.0 ◽  
Short Tandem

SummaryWe describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci.Availability and implementationExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/[email protected]

scholarly journals DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization

2021 ◽  
Author(s):  
Harrison Green ◽  
Jacob D. Durrant
Keyword(s):  
Deep Learning ◽  
Open Source ◽  
Early Stage ◽  
Molecular Structures ◽  
Lead Optimization ◽  
Third Party ◽  
Link Type ◽  
Version 2.0 ◽  
User Friendly ◽  
Deep Learning Model

1AbstractLead optimization, a critical step in early-stage drug discovery, involves making chemical modifications to a small-molecule ligand to improve its drug-like properties (e.g., binding affinity). We recently developed DeepFrag, a deep-learning model capable of recommending such modifications. Though a powerful hypothesis-generating tool, DeepFrag is currently implemented in Python and so requires a certain degree of computational expertise. To encourage broader adoption, we have created the DeepFrag browser app, which provides a user-friendly graphical user interface that runs the DeepFrag model in users’ web browsers. The browser app does not require users to upload their molecular structures to a third-party server, nor does it require the separate installation of any third-party software. We are hopeful that the app will be a useful tool for both researchers and students. It can be accessed free of charge, without requiring registration, at http://durrantlab.com/deepfrag. The source code is also available at http://git.durrantlab.com/jdurrant/deepfrag-app, released under the terms of the open-source Apache License, Version 2.0.

scholarly journals DrawAlignR: An interactive tool for across run chromatogram alignment visualization

2020 ◽  
Author(s):  
Shubham Gupta ◽  
Justin Sing ◽  
Arshia Mahmoodi ◽  
Hannes Röst
Keyword(s):  
Open Source ◽  
Web Application ◽  
Source Code ◽  
Link Type ◽  
Interactive Tool ◽  
Cumulative Score ◽  
Alignment Algorithms ◽  
R Shiny ◽  
Software Platforms

AbstractMulti-run alignment is widely used in proteomics to establish analyte correspondence across runs. Generally alignment algorithms return a cumulative score, which may not be easily interpretable for each peptide. Here we present a novel tool, DrawAlignR, to visualize each chromatographic alignment for DIA/SWATH data. Furthermore, we have developed a novel C++ based implementation of raw chromatogram alignment which is 35 times faster than the previously published algorithm. This not only enables users to plot alignment interactively by DrawAlignR, but also allows other software platforms to use the algorithm. DrawAlignR is an open-source web application using R Shiny that can be hosted using the source-code available at https://github.com/Roestlab/DrawAlignR.

Sign in / Sign up

Export Citation Format

Share Document