I have written a R code for Smith-Waterman (SW) algorithm.
I wanted to check the results of my code with online examples. In all cases -except one- I found the same alignment. So there is this one example -let's say example A*- for which I found a quite different alignment result: in the example they give three equivally good alignments whereas I found only one that corresponds to no none of those three alignments (we have the same score, though).
I am now trying to understand whether example A is wrong or if my code is not working properly.
Therefore, I have two requests:
- Does anyone have a dataset of the result of SW used on two sequences? I could then compare these results with the output of my code.
- Does anyone have whatever way to compute SW algorithm? Then, I could give that person the example A, which could then try this example A, and give me the output.
This would be very helpful if someone could help, I have already spent so much time on my code, without finding anything that could explain those different outputs.
- Example A: Sequence A = "TGCTCTGT" and Sequence B = "TACTATCAT"