Dear all,

I ran into the following problem: for some reason one sequence (Accession number: MN603925.1) does not seem to align properly, using the DECIPHER package. As shown in the image, the entire sequence ought to move one nucleotide to the right...

So far, I have not been able to solve this (2nd day using DECIPHER, and recently started with R). CorrectFrameshifts doesn not appear to solve it either.. (same output).

Could you give me any tips on how to solve this, or tell me what I am doing wrong?

Thank you in advance. Best wishes.

Max

setwd("<<working directory>>")

#I download the following 3 accession numbers (i.e. FASTA files; gene: 23s) from GENBANK nucleotide to my directory manually (https://www.ncbi.nlm.nih.gov/genbank/)
#Accession no: 
#CP018052.1  https://www.ncbi.nlm.nih.gov/nuccore/CP018052.1?from=862429&to=865374
#CP006945.1  https://www.ncbi.nlm.nih.gov/nuccore/CP006945.1?from=858226&to=861171
#MN603925.1  https://www.ncbi.nlm.nih.gov/nuccore/MN603925.1

# Open FASTA files (in quotes) and store in variable
fas1 <- readDNAStringSet("CP018052.1.fasta") 
fas2 <- readDNAStringSet("CP006945.1.fasta") 
fas3 <- readDNAStringSet("MN603925.1.fasta") 
Seqs <- c(fas1, fas2, fas3)

alignment <- AlignSeqs(Seqs)

BrowseSeqs(alignment)


#Correct frameshifts
REF <- translate(fas1)
correct <- CorrectFrameshifts(myXStringSet= fas3,
                               myAAStringSet=REF,
                               type="both")
fas3 <- correct$sequence
Seqs <- c(fas1, fas2, fas3)
alignment <- AlignSeqs(Seqs)
BrowseSeqs(alignment)               #same output.... 

sessionInfo( )
R version 4.0.3
DECIPHER_2.18.1
Biostrings_2.58.0
XVector_0.30.0
IRanges_2.24.0
S4Vectors_0.28.0
BiocGenerics_0.36.0
BiocManager_1.30.10

This is more likely an issue with your web browser's display of the alignment. Even though the displayed characters are all supposed to be the same width (i.e., fixed width font), some browsers do not adhere to this exactly. Try using another web browser and seeing if the problem goes away.

Thank you Erik, it solved the problem. I was using Microsoft Edge. When using Mozilla Firefox, the above problem doesn't occur.

Best regards,

Max