**25k**wrote:

Hi all,

I've a simple but intriguing question: I was trying to pull the BLOSUM80 matrix online, and I see that the substitution scores differ among sources.

For example, the Ter scores on this matrix are `-8`

while the same change on this NCBI BLOSUM80 are `-6`

Is there a "right" matrix? What do these different scores indicate as an underlying factor? I'd appreciate the community's input on this please.

Thank you!

This may also be related to the miscalculation discovered in BLOSUM matrices a few years back. Surprisingly miscalculated matrix was found to be better for searches.

76kSort of scary this observation, since it will eventually affect the results

4.3k