barto {genoPlotR} | R Documentation |
Comparison of 4 Bartonella genomes
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_segs
which is a list of 4dna_seg
objects, containing all the protein genes for each genome. Obtained by reading ptt files downloaded from NCBI withread_dna_seg_from_ptt
.comparisons
which is a list of 3comparison
objects, obtained by doing genome-to-genome (fasta files) BLASTS, and then reading the resulting tab files withread_comparison_from_blast
.rnt_segs
which is a list of 4dna_seg
objects, containing all the RNA genes of the four genomes. Obtained by reading rnt files downloaded from NCBI withread_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")