This repo is a start of a protein alignment using structural informations project.
The Needleman-Wunsch algorithm is written in Needle.py. There are differents variations of this algorithm, which are :
- gap, substitution and identification score
- scoring matrix (example : blosum62)
- affine gap penality, which can be from fixed scores or a scoring matrix
In Needle.py you can also find a method based on UPGMA (explained on wikipedia here) to make an alignment of many structures.
At the end of the notebook you can find a code that take superpose 2 proteins given in 2 differents orientations. This is the first step to use the structural informations to align the sequences.
Using 2 proteins structures, the score of each step in the Needleman-Wunsch can be updated. For example, add a function of the distance between two amino acids.