SynMut: Tools for Designing Synonymously Mutated Sequences with Different Genomic Signatures

Haogao Gu, Leo L.M. Poon

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This work was conducted in School of Public Health, The University of Hong Kong under the supervison of Prof. Leo Poon.

DOI: 10.18129/B9.bioc.SynMut

Introduction

SynMut designs synonymous mutants for DNA sequences.

There are increasing demands on designing virus mutants with specific dinucleotide or codon composition. This tool can take both dinucleotide preference and/or codon usage bias into account while designing mutants. It also works well for desinging mutants with extremely over-/under- represented dinucleotides.

This tool was originally designed for generating recombinant virus sequences in influenza A virus to study the effects of different dinucleotide usage and codon usage, yet the functions provided in this package can be generic to a variety of other biological researches.

Components of the package

SynMut component flowchart

Installation

Use the below code to install the package.

# Stable version
if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")

if (!requireNamespace("SynMut"))
    BiocManager::install("SynMut")

# Development version
if (!requireNamespace("devtools"))
    install.packages("devtools")

if (!requireNamespace("SynMut"))
    devtools::install_github("Koohoko/SynMut", ref = "devel")

Example and methods

Details tutorial please refer to the vignette.

The strategies and functionalities of the codom_mimic and dinu_to functions can be found at here.

Find it at Bioconductor

https://bioconductor.org/packages/devel/bioc/html/SynMut.html

Maintainer checklist

  1. Fetch both remotes and start from the current Bioconductor upstream/devel. Record the source commit and package version. Review GitHub-only changes separately; the package maintenance branch is devel on both remotes. Bump the patch version and update inst/NEWS before the final build.
  2. Use the R version appropriate for Bioconductor devel and a dedicated package library containing all Imports and Suggests. Check BiocManager::valid() and install Pandoc and TeX for the vignette and PDF manual.
  3. Download the current build environment settings to a separate file and select it with R_ENVIRON_USER for build/check sessions. Set R_LIBS_USER to the dedicated library; keep these settings out of the global R configuration.
  4. In a temporary directory, build a clean source copy with R CMD build --keep-empty-dirs --no-resave-data --md5 SynMut, then run R CMD check --timings SynMut_<version>.tar.gz. Keep the complete logs and session information. Include tests, examples, vignettes and the PDF manual.
  5. Rebuild a clean copy with network access disabled after installing dependencies. Confirm that the source archive contains vignettes/images/component.png and that the generated HTML embeds a valid PNG. Open the HTML to inspect the flowchart; a successful build alone does not prove images are valid.
  6. Review the final diff and checks before publishing the tested commit to both remotes' devel branches. Check the official build report after 24-48 hours. Match its version and commit to the published update, and inspect the distributed vignette again. Save raw logs immediately if a failure occurs because the latest report is overwritten by subsequent builds.

Changelog

Changes in version 1.1.5 (2022-06-03)

Changes in version 1.1.4 (2020-11-12)

Changes in version 1.1.3 (2019-05-08)

Changes in version 1.1.2 (2019-05-08)

Changes in version 1.1.1 (2019-05-06)