A BLASTn-based tool for pairwise genomes comparison (https://github.com/drostlab/metablastr).
install.packages("devtools")
library(devtools)
devtools::install_github('Mordziarz/transgenomes')
library(transgenomes)To use all features of the program, you will need several libraries.
library(metablastr)
library(circlize)The transfer_function() function accepted two FASTA files (fasta_q and fasta_s) along with two BED files containing gene annotations (bed_q and bed_s). The evalue_cutoff parameter was used to specify the E-value threshold for BLAST results.
The bed should look like this: V1 - Genome name, V2 - Start annotation, V3 - End annotation, V4 - Gene name
| V1 | V2 | V3 | V4 |
|---|---|---|---|
| Mitogenome | 0 | 74 | trnD1 |
| Mitogenome | 270 | 342 | trnN |
transfer_function(fasta_q = "fasta_q.fasta",
fasta_s = "fasta_s.fasta",
bed_q = bed_q,
bed_s = bed_s,
evalue_cut_off = 0.0001)The transfer_function() function produced an output table enriched with annotations for genes that had undergone partial or complete transfer to the second genome. The q_genes and s_genes columns within this table provided details about these transfers. For instance, the entry "genes: atp1 (1530)/(790)" indicated that the gene atp1, with a total length of 1530 nucleotides, had been transferred, and the transferred portion was 790 nucleotides long.
The program generated a basic visualization using the circlize package (https://github.com/jokergoo/circlize). This visualization was created based on the output from the transfer_function() function.
plot_transfers(transfer_function_out = transfer_function_out,
gap=40,
start_degree=90,
transparency=0.7)Useful functions for image cleaning in R
dev.off()
circlize::circos.clear()
Paper in preparation
Any issues connected with the transgenomes should be addressed to Mateusz Mazdziarz (mateusz.mazdziarz@uwm.edu.pl).