Answers.Body: <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>
  
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Answers.CreationDate: 2018-09-29T20:06:36.537Z
Answers.LastActivityDate: 2018-09-29T20:06:36.537Z
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Body: <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>
  
Tags: <blast><bitscore>
Title: Calculating bit score: How do you find lambda and K?
ThreadText: # Calculating bit score: How do you find lambda and K?
  
  (Asked by: username_0 on 2018-09-28)
  
  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?
  
  **Tags:** blast, bitscore
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2018-09-29. Score: 3 | Accepted answer
  
  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](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.7.1+-src.tar.gz).
  
  
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