Open donkirkby opened 8 years ago
@ArtPoon, I think you were working on a new alignment library that might replace Gotoh. Is that still happening, or should I dig into the Gotoh algorithm we have?
https://github.com/ArtPoon/gotoh2
I never got around to finishing it but a lot of the implementation is there.
Best, Art
Sent from my iPhone
On Dec 14, 2016, at 6:38 PM, Don Kirkby notifications@github.com wrote:
@ArtPoon, I think you were working on a new alignment library that might replace Gotoh. Is that still happening, or should I dig into the Gotoh algorithm we have?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.
While trying to write a test for issue #299, I discovered strange behaviour in the Gotoh alignment algorithm that we're using. Here's a small script to reproduce the problem:
The results are:
If I replace the E's with H's, I get this:
I understand that some substitutions are more likely than others, but why would it behave differently at the start and the end? If
gap_open + gap_extend <= 10
, then it opens a gap at both ends for E, and if it's less than or equal to 5, then it opens a gap for H.