nsrgenomes

Contents

Description
Installing nsrgenomes
Using nsrgenomes

Description

Generate formatted genome files for the OligoRL tool, NSR-RL.

Installing nsrgenomes

nsrgenomes is an R package. To install nsrgenomes run the following R code.

install.packages("BiocManager")
BiocManager::install("genbankr")
install.packages("devtools")
devtools::install_github("jensenlab/primer3")
devtools::install_github("https://github.com/bmdavid2/nsrgenomes")

Using nsrgenomes

Loading the nsrgenomes library will bring all necessary dependencies into the workspace. The function nsrgenomes downloads and formats genomes taken from the NCBI database.

nsrgenomes(species_name,accession_number)

Arguments

• species_name: Name of the organsim as a string, ex. "E_coli"

• accession_number: Accession number for the organism as a string, ex "NC_000913.3". Accesion numbers can be found at the NCBI website by searching the organsim of interest.

Output

the nsrgenomes automatically saves two .csv files in the working directory containing the formatted genomic information used by OligoRL's NSR-RL tool.

• species_name_genes.csv contains the list of mRNA sequences and other supplementary information used by the NSR-RL tool

• species_name_rRNA_tRNA.csv contains the list of all rRNA and tRNA sequences. These sequences will be avoided by NSR-RL.

Example

The following code is an example showing how to download the E coli K-12 genome files.

library(nsrgenomes)
nsrgenomes("E_coli","NC_000913.3")