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| The score for a word pair is |
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| the sum of the scores for each |
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| pair of residues |
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| • | Matching words
scoring above a threshold (T) |
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| are retained for
further analysis |
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| – | DNA: T = 0 |
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| – | Protein: T = 11 |
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| • | Stretches of
similarity are called HSPs (high- |
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| scoring segment
pairs) |
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