Hello there! I am new to Biostrings and have what is likely a simple question, but I can't seem to figure out a solution to this issue.
I am doing global pairwise alignments using pairwiseAlignment.
I have an example where the alignment results in three gaps at the start of the sequence. EX:
> align Global PairwiseAlignmentsSingleSubject (1 of 1) pattern: ---FLVLLPLVSSQCVNLTTRTQ...GSCCKFDEDDSEPVLKGVKLHYT subject: MFVFLVLLPLVSSQCVNLTTRTQ...GSCCKFDEDDSEPVLKGVKLHYT score: 5433.158 > pattern(align)  FLVLLPLVSSQCVNLTTRTQLPPA...GSCCKFDEDDSEPVLKGVKLHYT > subject(align)  FLVLLPLVSSQCVNLTTRTQLPPA...GSCCKFDEDDSEPVLKGVKLHYT
I am in need of having the full sequences including leading gaps (as well as corresponding positions in the subject/reference sequence).
I have discovered how to get the pattern as desired...
> as.character(align)  "---FLVLLPLVSSQCVNLTTRTQ...VLKGVKLHYT
but I can not figure out how one would do this with the subject/ref sequence. I have scoured the documentation, but must be missing something.
If anyone has advice, it would be greatly appreciated!