How to align two (or multiple) sequences, one (or part) of which is segmented?

Question

[luozx19]

How to align two (or multiple) sequences, one (or part) of which is segmented? For example, given the following two sequences

AABBBC

DBBBC

If I know that the segmentation of the first is

AA | BBB | C

I want to align these two sequences while keeping the original segment of the first sequence. Is there any algorithm supporting this? Thanks!

[Joe]

I believe Clustal supports something like this for concatenated alignments. You can provide it an 'index' file, of where the joins between "segments" in your words would be.

Not sure if this is entirely what you're after but sounds similar.