barto: Comparison of 4 Bartonella genomes

In genoPlotR: Plot Publication-Grade Gene and Genome Maps

Description

Comparison of 4 Bartonella genomes by BLAST.

Usage

data(barto)

Format

barto, a list of three dataframes, representing the four genomes and their pairwise comparisons:

• dna_segswhich is a list of 4 dna_seg objects, containing all the protein genes for each genome. Obtained by reading ptt files downloaded from NCBI with read_dna_seg_from_ptt.

• comparisonswhich is a list of 3 comparison objects, obtained by doing genome-to-genome (fasta files) BLASTS, and then reading the resulting tab files with read_comparison_from_blast.

• rnt_segswhich is a list of 4 dna_seg objects, containing all the RNA genes of the four genomes. Obtained by reading rnt files downloaded from NCBI with read_dna_seg_from_ptt.

A bash script to obtain the same file as in the dataset is available in the extdata folder of the package. Find its location by running system.file('extdata/barto.sh', package = 'genoPlotR').

References

BLAST: http://www.ncbi.nlm.nih.gov/blast/

Examples

data(barto)
plot_gene_map(barto$rnt_segs, barto$comparisons, gene_type="blocks")

Example output

Loading required package: ade4
Loading required package: grid

genoPlotR documentation built on Jan. 5, 2021, 3:02 p.m.