text: user3429: 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?
  
  user1802: 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.
  
original_text: 3429: <p>To calculate bitscore from score you can use this equation: <span class="math-container">$S' = (lambda*S - ln(K)) / ln(2)$</span></p>
  
  <p>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?</p>
  
  <p>Is there a more simple equation for pairwise nucleotide alignments?</p>
   1802: <p>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.</p>
  
  <p>You can find these tables (from line 589 for blastn) in the file <code>c++/src/algo/blast/core/blast_stat.c</code> from the <a href="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.7.1+-src.tar.gz" rel="nofollow noreferrer">blast source package</a>.</p>
  