ggmsa: a visual exploration tool for multiple sequence alignment and associated data

Abstract

The identification of the conserved and variable regions in the multiple sequence alignment (MSA) is critical to accelerating the process of understanding the function of genes. MSA visualizations allow us to transform sequence features into understandable visual representations. As the sequence–structure–function relationship gains increasing attention in molecular biology studies, the simple display of nucleotide or protein sequence alignment is not satisfied. A more scalable visualization is required to broaden the scope of sequence investigation. Here we present ggmsa, an R package for mining comprehensive sequence features and integrating the associated data of MSA by a variety of display methods. To uncover sequence conservation patterns, variations and recombination at the site level, sequence bundles, sequence logos, stacked sequence alignment and comparative plots are implemented. ggmsa supports integrating the correlation of MSA sequences and their phenotypes, as well as other traits such as ancestral sequences, molecular structures, molecular functions and expression levels. We also design a new visualization method for genome alignments in multiple alignment format to explore the pattern of within and between species variation. Combining these visual representations with prime knowledge, ggmsa assists researchers in discovering MSA and making decisions. The ggmsa package is open-source software released under the Artistic-2.0 license, and it is freely available on Bioconductor (https://bioconductor.org/packages/ggmsa) and Github (https://github.com/YuLab-SMU/ggmsa).

First detection of Ixodiphagus hookeri (Hymenoptera: Encyrtidae) in Ixodes ricinus ticks (Acari: Ixodidae) from multiple locations of Hungary

“…Multiple sequence alignment was done by MAFFT (v7.490) 35 . All data management procedures, analyses and plottings 36,37 were performed in R environment (v4.2.1). 38…”

High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny

“…All statistical analysis was performed in R v4.0.3. Phylogenetic trees and tp0470 and arp variants were visualized with the R packages ggtree ( Yu et al, 2017 ), treeio ( Wang et al, 2020 ), and ggplot ( Wickham, 2016 ), and multiple sequence alignments by R package ggmsa ( Zhou et al, 2022 ). Bash, R, and python scripts for all data processing are available at https://github.com/greninger-lab/TP_genome_finishing .…”

Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR

“…The pipeline consists of several steps: i) BlastP for homology searching (Camacho et al, 2009) with cut-offs set on a protein by protein basis to optimise numbers and diversity of hits: 50% sequence identity to the query cutoff for CplR (WP_011861613.1), 70% identity cutoff for VmlR (WP_003234144.1) and VmlR2 (WP_024026878.1) and 80% for LsaA (WP_002398829.1), ii) retrieval of 300 nt upstream sequences preceding the identified ARE-ABCF genes, iii) uORF annotation and, finally, iv) conservation analysis and multiple sequence alignment with MAFFT v7.490 (Katoh and Standley, 2013). Visualisation was performed with the ggmsa R package (Zhou et al, 2022), msa4u (Egorov and Atkinson, 2022) and Logomaker (Tareen and Kinney, 2020) Python packages. Secondary structures of the cplR 5ʹ leader region were predicted using RNAfold (Gruber et al, 2008) and Mfold (Peltier et al, 2020).…”