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Fig. 2 | BMC Genomics

Fig. 2

From: FuSpot: a web-based tool for visual evaluation of fusion candidates

Fig. 2

Smith Waterman Alignment Algorithm. (Scoring) Smith-Waterman alignment score matrix for the example read sequence, A, (given in the left-most column) against an example reference sequence, B (given in the top-most row) with the indicated scoring scheme. Each entry of the first row and first column are initialized to 0. Then each subsequent matrix element is calculated by taking of the maximum of the following three values: (1) Value of immediate left entry plus Gap Scoring Function, (2) Value of immediate top entry plus Gap Scoring Function, (3) Value of immediate top-left diagonal entry plus Similarity Function. (Backtrack) A tracing of the backtrack mechanism resultant from the above score matrix. Backtracking begins at the maximum matrix element (green) and continues to the matrix element from which its score was derived as defined by the scoring scheme. Movements to the diagonal produce a match or mismatch, movements to the top produce an insertion in the read, and movements to the left indicate a deletion in the read. This backtrack produces the alignment: Read: A _ C G T G A T; Reference: A C C G T C A T

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