Entering edit mode
10.0 years ago
crivenster
▴
50
Hi,
I have a local alignment on similar sequences using Smith-Waterman algorithm. I have alignment scores generated,how to calculate the percentage identity between the sequences? can it be calculated from the alignment score?
Thanks.
Unfortunately, it is not possible to precisely compute the identity merely from a score.
What software have you used to calculate the alignment?
I have written a small piece of code, implemented Smith-Waterman algorithm in java as i had some issues with Biojava package. But then i wanted to also find the percentage identity between the sequences. The online searches dint give a clear or a definite picture on calculating the percentage identity between two nucleotide sequences.