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][1] are `-8` while the same change on this [NCBI BLOSUM80][2] 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!


  [1]: http://www.cbcb.umd.edu/confcour/Fall2008/CMSC423-materials/BLOSUM80
  [2]: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM80
It looks like the two versions are using different units. In the first matrix the unit is 1/3 bit, while in the second matrix, it's 1/2 bit.

From the second matrix:

    a scale of ln(2)/2.0

is the conversion factor for 'nats' to half bit units.