I want to align a small sequence S1 to another larger nucleotide sequence S2 for example:
S1: acgtgt
S2: ttcgtgacagt...
In this example s1 hit in 2 places in s2 : cgtg and acgt with gap in s2 the 2. I want to use smith waterman algorithm but my question is : in case the 2 alignments have 2 diffrent score i.e one 4 and another 3 how to get the2 alignments from the dynamic programimg matrix? Is there any tool or library that do this already? I tried paorwise2 from biopython and it only gives the alignments with high score in tje matrix