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Choosing a Scoring Matrix

Choosing a Scoring Matrix: All the scoring matrices will not perform similarly and may not be suitable in every situation. As noted above, Johnson and Overington compared results obtained with 12 difference scoring matrices, and Pearson also recently published a comparison of several scoring methods some scoring matrices perform well in a situation than others which may fail to perform in other situations. So according to the requirement we have to select the scoring matrices, algorithm and local/global alignment. The advantage of local alignment over global is they don’t make any assumptions that the unknown protein and database are of similar length.

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