This is an R package to perform pairwise alignments of strings and plot them in a minimal style that is suitable for strings/sequences of any length. It is compatible with ggplot2 and DNA/AA sequence objects from Biostrings.
I recommend installing ggseqalign from Bioconductor.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ggseqalign")
ggseqalign can be installed from its original source on GitHub (requires devtools).
install.packages("devtools")
devtools::install_git("https://github.com/simeross/ggseqalign.git")
If you use any R version older than 4.4.0, install version 0.1.0 of this package.
install.packages("devtools")
devtools::install_git("https://github.com/simeross/ggseqalign@e1a2e99ee7d079d2e4331bc101382cfebe125fa8")
All you need is this package and some strings to align and you are ready to go.
library(ggseqalign)
query_strings <- (c("boo", "fibububuzz", "bozz", "baofuzz"))
subject_string <- "boofizz"
alignment <- alignment_table(query_strings, subject_string)
plot_sequence_alignment(alignment)
To align DNA or AA sequences from a fasta file, read them in with Biostrings
library(ggseqalign)
library(Biostrings)
query_sequences <- Biostrings::readDNAStringSet("my_multi_sequence_fasta.fa")
subject_sequence <- Biostrings::readDNAStringSet("my_reference_fasta.fa")
alignment <- alignment_table(query_sequences, subject_sequence)
pl <- plot_sequence_alignment(alignment)
pl
To style the plot generated above to your own taste, use ggplot2, for example:
library(ggplot2)
pl +
ylab("Sequence variants") +
xlab("Length in bp") +
scale_color_viridis_d() +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1),
axis.title = element_text())
If you come across bugs, please submit an issue
Artistic License 2.0.
The research and data generation that was a major motivation for me to finally create this package has received funding from the Norwegian Financial Mechanism 2014-2021, project DivGene: UMO-2019/34/H/NZ9/00559