Thank you mrbobly. I got the first error message again.
The file is a fasta file and is not authorized to be upload here. Maybe I will just give the lint to the web page.
I want to align the first two sequences using the command
pairwiseAlignment(pattern=seq2, subject=seq1)
only. Later I will be modifying to see how other factors affect the alignment.
It is actually a course in which I am learning to use R. So far everything was okay but at this point I got stuck.
These are the steps I followed
#Download the pro.fasta file into my working directory
Libraries
library(Biostrings)
library(seqinr)
prokaryotes <- read.fasta(file = "prok.fasta", seqtype = "DNA")
#Split first two sequences into individual sequences
seq1<-as.character(prokaryotes[[1]])
seq1=paste(seq1,collapse="")
seq2<-as.character(prokaryotes[[2]])
seq2=paste(seq2,collapse="")
#aligned the two sequences using the default libraries
pairwiseAlignment(pattern=seq2, subject=seq1)
I got the two sequences as strings but error in pairwiseAlignment