Derivative-free neural network for optimizing the scoring functions associated with dynamic programming of pairwise-profile alignment.
- Kazunori D Yamada
Algorithms Mol Biol 2018 15;13. Epub 2018 Feb 15.
1Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan.
Background: A profile-comparison method with position-specific scoring matrix (PSSM) is among the most accurate alignment methods. Currently, cosine similarity and correlation coefficients are used as scoring functions of dynamic programming to calculate similarity between PSSMs. However, it is unclear whether these functions are optimal for profile alignment methods. Read More