**10**wrote:

I have been trying to find an efficient way to find the suboptimal alignments given two sequences.

I understand that we can use Needleman-Wunsch algorithm to find optimal alignments but what about suboptimal alignments?

Is there a way to find suboptimal alignments?

Could we use forward algorithm to find suboptimal alignments?

Lets say we have the following two sequences

AAGTC AGGTC

**9.0k**• written 3 days ago by trinityduke100 •

**10**

~~https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm~~134kBut what I understand is that Smith-Waterman algorithm is for local alignment and not for global alignment?

10ah ok, I misunderstood your question. For a global alignement, when back-scanning the matrix, you can explore the alternate ways to build the best alignment instead of following the 'best' path.

134kBut given that there are exponentially large number of possible alignments, isn't there any efficient alternative?

10