I'm coding a pipeline where I make a lot of pairwise alignments, and I end up with raw alignment scores. But, I really need to look at my results in terms of bit scores.

I know that the formula is:

$𝑆′ = (ƛ*𝑆 − 𝑙𝑛(𝐾)) / 𝑙𝑛(2)$

But, I don't know what ƛ or K would be. I'm currently using BLOSUM62.

I've looked around online for how to look up (and even empirically deduce) lambda and k, and I all I've come across were convoluted explanations.

I also know that this question from almost 3 years ago attempts to address the same topic, but the best response only leads to an NCBI link that requires login credentials.

Any help would be much appreciated.


Answer from @terdon, converted from comment:

The link just points to the NCBI ftp site where you can download the source package and look at the code. There is no need for login credentials, you can log in as anonymous. It's just that the version has changed so that answer's URL no longer works. Try this instead:

wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.11.0+-src.tar.gz

Then, extract the files and look at the file c++/src/algo/blast/core/blast_stat.c which, again according to the answer you linked to, should have the lamda and k tables at line 589.


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