Here we present an interactive example of the Needleman-Wunsch global alignment algorithm from BIMM-143 Class 2. The purpose of this app is to visually illustrate how the alignment matrix is constructed and how the Needleman-Wunsch dynamic programing algorithm fills this matrix based on user defined Match, Mismatch and Gap Scores. Note that for improving your understanding of this algorithm there is no substitute for working this out for yourself with pen and paper as we did on the white-board together in class!
Experiment by changing the various Scores, altering the two Sequences and noting how the alignment matrix values, trace back alignment path (in red), and overall alignment score change.
Details:
Mousing over the matrix itself will show you how the individual values are calculated (based on the highlighted scores in the previous 3 cells of the matrix) and how different paths through the matrix translate into the final alignment. Finally, you can also construct a 'Custom Path' through the matrix by selecting the 'Custom Path' button and clicking on a connected series individual matrix cells to see how your trace back path through the matrix translates into a particular alignment with various path dependent matches, mismatches and gaps.
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