I have a AAstringSet. Some of them have stop codon that I need to filter out and the aastring need to fit to my pattern LVXXXLXXXL, X in IUPAC code, represent any amino acids.
stopcodon = vmatchPattern("*",seqs.frame$aa,max.mismatch=0)
I have the index of the AAStrings now, but how do I get rid of them from the seqs.frame ?
I guess I can use vmatchPattern again with for the LVXXXLXXL once the above is figured out.