Handling biological sequences in R with thebioseqpackage

摘要

With the democratization of molecular biology, more and more ecologists are required to analyse complex datasets including biological sequences. I present the R packagebioseq, a comprehensive toolset to handle biological sequences in R. The package implements three classes to work with DNA, RNA and amino acid sequences. Biological sequences are stored as simple vectors of character strings with restricted alphabets. This storage mode makes it easy to work with dataframes. The package includes a collection of functions to perform basic editing operations on sequences and biological conversion among classes. The package can read and convert data from and to several formats. Thus, users can benefit from the richness of the R environment to perform advanced biological sequence analysis. Thebioseqpackage is a free software intended to be of significant value to researchers who need a simple and solid framework to analyse biological sequence data in R.