Smith waterman algorithm online dating

The yellow color indicates the bases that are being considered.

The red color indicates the highest possible score for the cell being scored.

The finished scoring matrix is shown below on the left. Note that an element can receive score from more than one element, each will form a different path if this element is traced back.

In case of multiple highest scores, traceback should be done starting with each highest score. The best local alignment is generated in the reverse direction.

The additional first row and first column serve the purpose of aligning one sequence to any positions in the other sequence.

The initial scoring matrix of Smith–Waterman algorithm enables the alignment of any segment of one sequence to an arbitrary position in the other sequence.The initial scoring matrix is: Initialize and fill the scoring matrix, shown as below.This figure shows the scoring process of the first three elements.The scoring process reflects the concept of dynamic programming.The final optimal alignment is found by iteratively expanding the growing optimal alignment.

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