Dear all,

I want to align circular sequences (plasmids, > 10000 bp) to check if they are identical or to see where they differ.

Due formatting by other software, sequences do not necessarily start at the same position. But other than different starts they may be identical. The sequences are just shifted so to say.

Question is: How to elegantly use Biostrings::pairwiseAlignment() for such problem?

I believe the DNAString oder DNAStringSet does not handle circular sequences ...

Thanks.