Re: Jan. 27 BioMOO session

David Cavanaugh (
Fri, 5 Feb 1999 23:59:12 -0600

At 12:07 AM 2/6/99 GMT, Gabor Mocz wrote:
>Hello Everyone,
>Still back to the Jan. 27 BioMOO session, ... I have found another
>reference on the relative performance of various amino acid scoring
>matrices. Here it is, in case you are interested:
>"An assesment of amino acid exchange matrices in aligning protein
>sequences: The twilight zone revisited"
>Vogt, G., Etzold, T., and Argos, P. 1995. J.Mol.Biol.249:816-831.

Here's some online resources, downloadable papers and tutorials on this subject.

I asked a question regarding the structure of the alignment distance
matricies. Some of these papers address that issue. Generally the pairwise
distance/scoring matrix has the form of the log of a probability.

- David