Albert-Ludwigs-Universität Freiburg
Lehrstuhl für Bioinformatik - Institut für Informatik - http://www.bioinf.uni-freiburg.de
a) Implement the function sw_init() which takes two sequences S1 and S2 and creates the Smith-Waterman matrix and initiates all the matrix values with zeroes. Hereby S1 should be represented by the rows and S2 by the columns.
b) Implement the function sw_forward() which takes the two sequences S1 and S2 and the scoring function and output the complete matrix filled with the Smith-Waterman approach.
The following steps will help you with implementing the traceback.
c) Implement the function previous_cells() which takes two sequences S1 and S2, scoring function, the filled in recursion matrix from the step b) and the cell coordinates as a tuple (row, column). The function should output a list of tuples of all possible previous cells. The tuples should be again structured like (row, column).
d) Implement the function which builds all possible traceback paths. This function should return a list of possible paths which themselves are a list of tuples (row, column). The ordering must be decreasing. Meaning paths should start in the lower right corner of the matrix.
e) Implement the function build_alignment() which takes two sequences and a path as a list of tuples. This function should return a local alignment tuple. Meaning two substrings with introduced gaps.