The GenBank BLAST Email Server uses defaults of 5 and -4 for parameters
M and N in blastn jobs. These are described as follows in its HELP file:
In blastn, M is the score for a single-letter match; N is
the score for a single-letter mismatch. M and N must be
positive and negative integers, respectively. Given the
assumption made by blastn that the 4 nucleotides A, C, G,
and T are represented equally in the database, the expected
score for the query sequence must be negative.
M (but apparently not N) can be changed by providing a value for MATCH in the
job submission file. What are the considerations and consequences associated
with changes from the default value of 5?
Fote
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