Re: Jan. 27 BioMOO session

David Cavanaugh (dcavanau@ro.com)
Fri, 5 Feb 1999 23:59:12 -0600

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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.

http://www.blocks.fhcrc.org/papers/
http://www.biochem.vt.edu/courses/modeling/homology.html
http://www.icgeb.trieste.it/net/courseware/basic.htm

- David

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