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To calculate bitscore from score you can use this equation: $S' = (lambda*S - ln(K)) / ln(2)$
If I am trying to manually calculate the bitscore of an HSP of a pairwise blastn alignment, and I know the alignment score, how do I calculate the parameters K and lambda?
Is there a more simple equation for pairwise nucleotide alignments?
NCBI BLAST uses tables of pre-computed values for lambda/K for gapped protein and nucleotide comparison and their values depend on the amino acid substitution matrix or the substitution scores + gap penalties.
You can find these tables (from line 589 for blastn) in the file c++/src/algo/blast/core/blast_stat.c from the blast source package.
