Hi Laksmi,

It's not quite clear from your questoin, but do you want to do a pairwise alignment of each of your 90 sequences against a particular sequence (ie seq2[[1]] v seq1 then seq2[[2]] v seq1 in your example) or you want to do all the possible pairwsie comparisons between your 90 sequences.

The first one is easy, use an apply function. I don't have bioconductor on this computer, so this isn't tested, but something like

sapply( seq2, function(x) pairwiseAlignment(toupper(c2s(x)), seq1string)) )

It's probably more readible if you define a function first:

convert_then_align <- function(a,ref_seq){
  seq_string <- toupper(c2s(a))
  return(pairwiseAlignment(seq_string, ref_seq))
}

sapply(seq2, convert_then_align, seq2string)

All possible combinations is a little tricker, the way I do these is to make the indices first:

all_pairs <- combn(1:length(seq2), 2)

Then you need a function to do your converting and aligning

align_from_index <- function(sequences, index.a, index.b){
  seq1 <- toupper(c2s(sequences[index.a]))
  seq2 <- toupper(c2s(sequences[index.b]))
  return( pairwiseAlignment(seq1, seq2) )
}

res <- apply(all_pairs, 2, function(indices) align_from_index(sequences, indices[1], indices[2]) )

Which you can turn into a matrix if pairwiseAlignment returns something that makes sense for that (there must be a less hacky way of doing this!):

attributes(res) <- attributes(dist(1:length(seq2))
res <- as.matrix(res)