Durrant, J. D. | bioRxiv Science

bioRxiv2020

MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations

MutantHuntWGS is a user-friendly pipeline for analyzing Saccharomyces cerevisiae whole-genome sequencing data. It uses available open-source programs to: (1) perform sequence alignments for paired and single-end reads, (2) call variants, and (3) predict variant effect and severity. MutantHuntWGS outputs a shortlist of variants while also enabling access to all intermediate files. To demonstrate its utility, we use MutantHuntWGS to assess multiple published datasets; in all cases, it detects the same causal variants reported in the literature. To encourage broad adoption and promote reproducibility, we distribute a containerized version of the MutantHuntWGS pipeline that allows users to install and analyze data with only two commands. The MutantHuntWGS software and documentation can be downloaded free of charge from https://github.com/mae92/MutantHuntWGS.

genetics↗

bioRxiv2019

Webina: An Open-Source Library and Web App that Runs AutoDock Vina Entirely in the Web Browser

1Molecular docking is a computational technique for predicting how a small molecule might bind a macromolecular target. Among docking programs, AutoDock Vina is particularly popular. Like many docking programs, Vina requires users to download/install an executable file and to run that file from a Unix- or DOS-like command-line interface. Choosing proper configuration parameters and analyzing Vina output is also sometimes challenging. These issues are particularly problematic for students and novice researchers. We have created Webina, a new version of Vina, to address these challenges. Webina is a JavaScript/WebAssembly library that runs AutoDock Vina entirely in a web browser. To use Webina, users need only visit a Webina-enabled webpage. The docking calculations take place on the users own computer rather than a remote server. To encourage use, we have incorporated the Webina library into our own Webina web app. The app includes a convenient interface so users can easily setup their docking runs and analyze the results. Webina will be a useful open-source tool for the research and educational communities. A working version of the app can be accessed free of charge from http://durrantlab.com/webina.

pharmacology and toxicology↗