[Computational-biology] Re: PAM matrices

Kevin Karplus karplus at cheep.cse.ucsc.edu
Mon May 30 13:13:03 EST 2005


On 2005-05-30, enrico <enrivarAT at fastwebnet.it> wrote:
> I need to compute arbitrary time PAM matrices (where time is continuous 
> and not discrete). I know that this is quite easy having the 
> instantaneous rate matrix (i.e. P(i,j,t) = exp(Q*t)). Unfortunatly I 
> wasn't able to find such rate matrix, is there someone who can help?

Perhaps 

Different Versions of the Dayhoff Rate Matrix
Authors: Carolin Kosiol; Nick Goldman
Source: Molecular Biology and Evolution, February 2005, vol. 22,
	no. 2, pp. 193-199(7)
Publisher: Oxford University Press

would help?

Otherwise you could go back to Dayhoff's 1979 paper to get the
original rate matrix.

------------------------------------------------------------
Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors, ISCB)
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Affiliations for identification only.




More information about the Comp-bio mailing list