<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>

CC BY-SA 4.0
2018-09-29T20:06:36.537Z
2018-09-29T20:06:36.537Z
Peter Menzel
<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>

<blast><bitscore>
Calculating bit score: How do you find lambda and K?
# 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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