Annotation

Annotation Introduction

For sequence annotations, ggmsa supports individual modules to annotate sequence alignments. Annotated modules can be called by a + prefix. Automatically generated annotations that containing colored labels and symbols are overlaid on MSAs to indicate potentially conserved or divergent regions.

Annotation modules	Type	Description
geom_seqlogo()	geometric layer	automatically generated sequence logos for a MSA
geom_GC()	annotation module	shows GC content with bubble chart
geom_seed()	annotation module	highlights seed region on miRNA sequences
geom_msaBar()	annotation module	shows sequences conservation by a bar chart
geom_helix()	annotation module	depicts RNA secondary structure as arc diagrams(need extra data)

geom_seqlogo

Protein sequence logos annotation for MSA. Sequence logos play a major role in visualizing DNA, RNA and protein binding sites. In the following example, geom_seqlogo() module is used to display sequence logos between 300 and 350 sites. The + can be used to link main function ggmsa() and geom_seqlogo() module.

ggmsa(protein_sequences, 300, 350, char_width = 0.5, seq_name = TRUE) + 
    geom_seqlogo(color = "Chemistry_AA")

geom_GC

geom_GC() module calculating the GC-content in DNA/RNA sequences. The sizes of bubbles are identical with GC-content.

nt_sequence <- system.file("extdata", "LeaderRepeat_All.fa", package = "ggmsa")
ggmsa(nt_sequence,font = NULL, color = "Chemistry_NT") + 
    geom_seqlogo(color = "Chemistry_NT") + geom_GC() + theme(legend.position = "none")

geom_seed

geom_seed() helps to identify microRNA seed region by asterisks or shaded area. The seed region is a conserved heptameric sequence that is mostly situated at positions 2-7 from the miRNA 5´-end.

ggmsa(miRNA_sequences, char_width = 0.5, color = "Chemistry_NT") + 
    geom_seed(seed = "GAGGUAG", star = TRUE)

ggmsa(miRNA_sequences, char_width = 0.5, seq_name = TRUE, none_bg = TRUE) + 
    geom_seed(seed = "GAGGUAG")

geom_msaBar

geom_msaBar shows the highest frequency of amino acid residues at each position by a bar chart.

ggmsa(protein_sequences, 300, 350, char_width = 0.5, seq_name = TRUE) + geom_msaBar()

geom_helix

ggmsa supports plotting RNA secondary structure as arc diagram by reference to R4RNA. For example, adding a structure arc above diagram multiple sequence alignment helps to identify the base pair conservation and co-variation.