¥Lambda and K are statistical
parameters used in calculating the significance of the gapped alignment score.
They are determined on the basis of the alignment scores of random sequences
using a combination of scoring matrix and gap penalties (Bioinformatics, D. W
Mount, page 251).
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¥H is the relative entropy that shows the ability of the
entire substitution matrix to discriminate related from unrelated
sequences.
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¥The scoring
matrix that was used
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¥The gap
creation/gap extension costs
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¥Values for various steps in the search process leading to the identification
of HSPs (High-scoring element pair).
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¥Calculated values for database size, query size, and so on used in the search.