I am trying to align different sequences and additionally to the aligned sequences, I would like to add an extra sequence of peptides matching sequence number 2 for example. The peptides and the matching positions I would get from MaxQuant software for example...

At the moment I am lacking the commands to add strings (sequences) to an existing alignment and adapt the start and end position.

library(msa)
mySequenceFile <- system.file("examples", "exampleAA.fasta", package="msa")
mySequences <- readAAStringSet(mySequenceFile)
myFirstAlignment <- msa(mySequences)

I can add my sequence (just a snippet for testing), building it by hand and add it manually to the StringSet, but I can not not overwrite the StringSet within the alignment. Of course, there is more adaptation needed.

append(myFirstAlignment@unmasked, subseq('RLFEEND-------END'))
append(myFirstAlignment@unmasked, subseq('RLFEEND-------END')) -> 
  myFirstAlignment@unmasked

My goal ist to use the msaPrettyPrinting function to print the MSA in nice colors and other functionality. But I would like to add my peptides detected in the mass spec.

Hope somebody can guide me a little, which modifications I need to do. Or maybe can suggest a better tool the have such a nice presentation as msaPrettyPrinting.

Best
Mario