| Step 2 - Initial searching |
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| • | Each word in the
probe sequence index |
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| is compared to
the database index and |
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| residue pairs are
scored |
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| • | For DNA sequences
a match is +1, a |
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| mismatch is - 3 |
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| • | For protein
sequences, scores for |
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| matches and
mismatches are based on |
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| a substitution
matrix |
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