barto {genoPlotR} | R Documentation |
Comparison of 4 Bartonella genomes by BLAST.
data(barto)
barto
, a list of three dataframes, representing the four genomes
and their pairwise comparisons:
dna_segs
which 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
.
comparisons
which 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_segs
which 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')
.
BLAST: http://www.ncbi.nlm.nih.gov/blast/
data(barto) plot_gene_map(barto$rnt_segs, barto$comparisons, gene_type="blocks")