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## SynMut: Tools for Designing Synonymously Mutated Sequences with Different Genomic Signatures *Haogao Gu, Leo L.M. Poon* <img src="" alt="drawing" width="200" ALIGN="LEFT" /> ##### 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]( <img border="0" src=""> ### 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 ![image]( ### Installation Use the below code to install the package. ```r # 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") ``` ### 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 *** ### Changelog Changes in version 1.1.5 (2022-06-03) + Enhancement: add other non-standard genetic codes for functions codon_random, dinu_to, codon_mimic. Changes in version 1.1.4 (2020-11-12) + bug fix: fix for function codon_mimic. Changes in version 1.1.3 (2019-05-08) + Revise dinu_to.keep algorithm, enhance performance. Changes in version 1.1.2 (2019-05-08) + Bug fix: "dinu_to" ifelse issue in get_optimal_codon. Changes in version 1.1.1 (2019-05-06) + Bug fix: "dinu_to" fix wrong result with "keep == TRUE" parameter.