Subject: Su: amino acid exchange matrices

From: "Dimitris Agrafiotis" <[email-masked]>
Date: Wed, 25 Sep 1996 10:30:46 -0400

As promised, I attach a summary of responses to my posting regarding
amino acid exchange matrices for protein sequence analysis.

______________________________________________________________________________

On Sep 17, 11:52am, Mark Johnson MOL wrote:
>
> Matrices, we have. I enclose our file from our www pages,
> about a dozen or so matrices, references our comparison papers.
> See Johnson & Overington 1993 JMB where we compared these matrices;
> Se all Vogt et al (1995) JMB 249, 816
> where they consider an even larger group of matrices.
>
> Good luck, Mark Johnson
>
> from html page ...
>
> Matrices for comparing sequences obtained from different published works.
> Includes Dayhoff 250 & 120 PAM matrices, Gonnet, Henikoff & Henikoff,
> Johnson & Overington 1993, Rao, and others.
>
> /*
>  *	MAY BE FREELY DISTRIBUTED WITH THE PERMISSION OF THE AUTHOR
>  *
>  *	As with most things in life, use is at your own risk (except
>  *	in the States where accidents and misfortunes are not permitted
>  *	under the lawyers' Bill of Free Enterprise).
>  *
>  *	Mark S. Johnson, Modelling and Biocomputing Group, Center
>  *	for Biotechnology, PO Box 123, FIN-20521 TURKU, FINLAND
>  *	FAX: 358-21-633-8000 Email: [email-masked]
>  *
>  */
>
> References:
>
> Johnson, M.S. & Overington, J.P. (1993).
> "A structural basis for the comparison of sequences: An
> evaluation of scoring methodologies." <I>J. Mol. Biol.<B> 233</B></I>,
716-738.
> <BR><BR>
> Johnson, M.S., Overington, J.P. & Blundell, T.L. (1993).
> "Alignment and Searching for Common Folds Using a Data Bank of Structural
> Templates."
> <I>J. Mol. Biol.</B></I>, <B>231,</B></I> 735-752.
> <BR><BR>
> Johnson, M.S., May, A.C.W., Rodionov, M.A. & Overington, J.P. (1996).
"Discrimination of common protein folds:
> applications of structural information to sequence/structure comparisons,"
> <I>Methods in Enzymology</B></I> <B>266</B></I>, 575-598.
> <BR><BR>
> Johnson, M.S, Overington, J.P., Edwards, Y., May, A. & Rodionov, M.A. (1994).
> "An integrated approach to the comparison of structures and sequences:
> alignment, searching and the detection of common folds."
> <I>Proc. 27th Hawaii Intern. Conf. Syst. Sci.<B> V</B></I>, 296-305.
> <BR><BR>
> Overington, J.P., Donnelly D., Johnson, M.S., \(vSali A. & Blundell, T.L.
> (1992). "Environmental specific amino acid substitution tables:
> tertiary templates and prediction of protein folds."
> <I>Protein Science<B> 1</B></I>, 216-226.
> <BR><BR>
> Overington, J.P., Johnson, M.S., \(vSali, A. & Blundell, T.L. (1990).
> "Tertiary constraints on protein evolutionary diversity: Templates,
> key residues and structural prediction."
> <I>Proc. Roy. Soc. London</B></I> B <B>241</B></I>,132-145.
> <BR><BR>
> <PRE>
> /* mat.h		msjohnson		*/
>  *	different matrices (PAM250 etc) including one based on 110
>  *	aligned 3D structures: STRMAT110
>  *      computed according to:
>  *		Johnson & Overington (1993) J. Mol. Biol. 233:716-738
>  *      see Johnson, Overington & Blundell (1993) J. Mol. Biol. 231:735-752.
>  *          Overington, Johnson, Sali & Blundell (1990) Proc. Roy. Soc.
London
>  *	    ser. B, 241:146-152.
>  *	    Sali & Overington (1994) Prot. Sci. 3:1582-1596.
>  */
>
> /*
> ##
> ##  TRADITIONAL DISCLAIMER
> ##
> ##  Copyright 1988-1996 John Overington & Mark Johnson
> ##
> ##  Permission to use, copy, modify, and distribute this data, software
> ##  and its documentation for academic purposes is hereby granted without
fee,
> ##  provided that the above copyright notice appear in all copies and that
> ##  both that copyright notice and this permission notice appear in
> ##  supporting documentation, and that the name of John Overington or Mark
> ##  Johnson or our respective institutions
> ##  not be used in advertising or publicity pertaining to distribution of
> ##  the software without specific, written prior permission. We
> ##  makes no representations about the suitability of this software for any
> ##  purpose. It is provided "as is" without express or implied warranty.
> ##
> ##  JOHN OVERINGTON  AND MARK JOHNSON DISCLAIM ALL WARRANTIES WITH REGARD TO
> ##  THIS SOFTWARE/DATA, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY
AND
> ##  FITNESS, IN NO EVENT SHALL OUR HOME INSTITUTIONS BE LIABLE FOR ANY
SPECIAL,
> ##  INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
FROM
> ##  LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
NEGLIGENCE
> ##  OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
> ##  OR PERFORMANCE OF THIS SOFTWARE.
> ##
> ##  Primary authors:
> ##  	Dr. John Overington
> ##      Pfizer Central Research
> ##  	Pfizer UK
> ##  	Sandwich, Kent, UK
> ##
> ##  	[email-masked]
> ##
> ##	Dr. Mark Johnson
> ##	Turku Center for Biotechnology
> ##	University of Turku & Abo Akademi University
> ##	PO Box 123
> ##	FIN-20521 Turku, Finland
> ##
> ##	[email-masked]
> ##
> ## Please send any improvements, bug fixes, useful modifications, and
comments
> ## to one of the addresses above
> */
>
>
> #define MAT_VER	"[matrix version 11.0 (last update: 24-11-95)]"
> #define MAX_MAT 15	/* Limit to matrices in mat10.h */
> #define MAX_VAL 21	/* Limit to dimensions in mat10.h */
>
> /*
>  *	B -> D (2); Z -> E (3); X (unknown) -> 21 == 0's in matrix
>  */
>
> int ind[MAX_IND]={ 0, 2, 1, 2, 3, 4, 5, 6, 7,21, 8, 9,10,
>                   11,21,12,13,14,15,16,21,17,18,21,19, 3};
>
> /*
> values in matrices are in alphabetical order (with the exception of X):
> 	ACDEFGHIKLMNPQRSTVWYX
>
> border of matrices: }, {
> */
>
> char m_names[MAX_MAT][MAX_CDE]=
>
> {"STRMAT110", "DAYHOFF", "DOOLITTLE", "FITCH", "GRANTHAM",
> "LEVIN", "MCLACHLAN", "MIYATA", "RAO", "RISLER", "GONNET",
> "HENIKOFF", "JONES", "PAM120", "TEST MATRIX"};
>
> /* m_100: scaled matrices; matrices follow in above order */
>
>
> int mats[MAX_MAT][MAX_VAL][MAX_VAL] = {
> {
> {65,10,43,45,37,45,38,38,44,38,42,42,45,43,38,46,44,46,30,35,0},
> {10,100, 7,16,20,11,18,14,11,14,19,20, 0,17,24,14,14,11,19,17,0},
> {43, 7,72,53,27,41,43,28,43,25,29,54,43,44,37,45,41,32,28,35,0},
> {45,16,53,72,31,40,43,33,48,31,37,45,42,53,43,41,42,36,28,35,0},
> {37,20,27,31,77,24,42,48,30,51,47,33,30,31,31,30,31,43,50,58,0},
> {45,11,41,40,24,71,37,24,37,25,29,42,36,35,37,41,33,29,31,32,0},
> {38,18,43,43,42,37,83,31,47,36,39,51,37,50,46,39,38,35,35,47,0},
> {38,14,28,33,48,24,31,72,32,53,54,33,33,30,32,32,40,58,36,40,0},
> {44,11,43,48,30,37,47,32,68,37,40,47,40,50,56,42,45,37,31,34,0},
> {38,14,25,31,51,25,36,53,37,68,59,32,33,37,38,30,35,51,39,39,0},
> {42,19,29,37,47,29,39,54,40,59,79,36,27,42,35,34,40,48,47,40,0},
> {42,20,54,45,33,42,51,33,47,32,36,70,41,44,45,49,46,33,31,41,0},
> {45, 0,43,42,30,36,37,33,40,33,27,41,77,37,37,42,40,35,25,32,0},
> {43,17,44,53,31,35,50,30,50,37,42,44,37,74,47,41,41,37,28,31,0},
> {38,24,37,43,31,37,46,32,56,38,35,45,37,47,76,42,42,35,37,36,0},
> {46,14,45,41,30,41,39,32,42,30,34,49,42,41,42,66,52,34,27,36,0},
> {44,14,41,42,31,33,38,40,45,35,40,46,40,41,42,52,68,42,23,34,0},
> {46,11,32,36,43,29,35,58,37,51,48,33,35,37,35,34,42,68,30,36,0},
> {30,19,28,28,50,31,35,36,31,39,47,31,25,28,37,27,23,30,91,52,0},
> {35,17,35,35,58,32,47,40,34,39,40,41,32,31,36,36,34,36,52,78,0},
> {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0},
> },{ /*dayhoff*/
> {40,24,32,32,16,36,28,28,28,24,28,32,36,32,24,36,36,32,8,20,0},
> {24,80,12,12,16,20,20,24,12,8,12,16,20,12,16,32,24,24,0,32,0},
> {32,12,48,44,8,36,36,24,32,16,20,40,28,40,28,32,32,24,4,16,0},
> {32,12,44,48,12,32,36,24,32,20,24,36,28,40,28,32,32,24,4,16,0},
> {16,16,8,12,68,12,24,36,12,40,32,16,12,12,16,20,20,28,32,60,0},
> {36,20,36,32,12,52,24,20,24,16,20,32,28,28,20,36,32,28,4,12,0},
> {28,20,36,36,24,24,56,24,32,24,24,40,32,44,40,28,28,24,20,32,0},
> {28,24,24,24,36,20,24,52,24,40,40,24,24,24,24,28,32,48,12,28,0},
> {28,12,32,32,12,24,32,24,52,20,32,36,28,36,44,32,32,24,20,16,0},
> {24,8,16,20,40,16,24,40,20,56,48,20,20,24,20,20,24,40,24,28,0},
> {28,12,20,24,32,20,24,40,32,48,56,24,24,28,32,24,28,40,16,24,0},
> {32,16,40,36,16,32,40,24,36,20,24,40,28,36,32,36,32,24,16,24,0},
> {36,20,28,28,12,28,32,24,28,20,24,28,56,32,32,36,32,28,8,12,0},
> {32,12,40,40,12,28,44,24,36,24,28,36,32,48,36,28,28,24,12,16,0},
> {24,16,28,28,16,20,40,24,44,20,32,32,32,36,56,32,28,24,40,16,0},
> {36,32,32,32,20,36,28,28,32,20,24,36,36,28,32,40,36,28,24,20,0},
> {36,24,32,32,20,32,28,32,32,24,28,32,32,28,28,36,44,32,12,20,0},
> {32,24,24,24,28,28,24,48,24,40,40,24,28,24,24,28,32,48,8,24,0},
> {8,0,4,4,32,4,20,12,20,24,16,16,8,12,40,24,12,8,100,32,0},
> {20,32,16,16,60,12,32,28,16,28,24,24,12,16,16,20,20,24,32,72,0},
> {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0},
> },{
> {100,33,67,67,33,83,33,33,50,33,33,50,83,50,33,83,83,83,33,33,0},
> {33,100,17,0,50,50,33,33,0,33,33,33,33,17,33,67,33,33,50,50,0},
> {67,17,100,83,17,67,50,17,50,17,0,83,33,67,33,50,33,50,0,33,0},
> {67,0,83,100,0,67,33,17,67,17,17,50,50,67,33,50,50,67,17,17,0},
> {33,50,17,0,100,17,33,67,0,67,33,17,33,17,17,50,17,67,50,83,0},
> {83,50,67,67,17,100,17,33,33,33,17,50,50,33,50,83,33,67,50,33,0},
> {33,33,50,33,33,17,100,17,50,50,17,67,50,67,67,50,33,17,17,50,0},
> {33,33,17,17,67,33,17,100,33,83,67,33,33,17,33,33,50,83,33,50,0},
> {50,0,50,67,0,33,50,33,100,33,33,67,33,67,83,50,67,50,17,17,0},
> {33,33,17,17,67,33,50,83,33,100,83,17,50,33,33,33,33,83,67,50,0},
> {33,33,0,17,33,17,17,67,33,83,100,17,33,33,33,17,50,67,50,33,0},
> {50,33,83,50,17,50,67,33,67,17,17,100,33,50,33,83,67,33,0,50,0},
> {83,33,33,50,33,50,50,33,33,50,33,33,100,50,50,67,67,50,33,33,0},
> {50,17,67,67,17,33,67,17,67,33,33,50,50,100,50,50,50,33,17,33,0},
> {33,33,33,33,17,50,67,33,83,33,33,33,50,50,100,50,50,33,33,17,0},
> {83,67,50,50,50,83,50,33,50,33,17,83,67,50,50,100,83,33,33,50,0},
> {83,33,33,50,17,33,33,50,67,33,50,67,67,50,50,83,100,50,17,33,0},
> {83,33,50,67,67,67,17,83,50,83,67,33,50,33,33,33,50,100,50,50,0},
> {33,50,0,17,50,50,17,33,17,67,50,0,33,17,33,33,17,50,100,50,0},
> {33,50,33,17,83,33,50,50,17,50,33,50,33,33,17,50,33,50,50,100,0},
> {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0},
> },{
> {100,25,50,50,25,50,25,25,25,25,25,25,50,25,25,50,50,50,25,25,0},
> {25,100,25,0,50,50,25,25,0,25,0,25,25,0,50,50,25,25,50,50,0},
> {50,25,100,50,25,50,50,25,25,25,0,50,25,25,25,25,25,50,0,50,0},
> {50,0,50,100,0,50,25,25,50,25,25,25,25,50,25,25,25,50,25,25,0},
> {25,50,25,0,100,25,25,50,0,50,25,25,25,0,25,50,25,50,25,50,0},
> {50,50,50,50,25,100,25,25,25,25,25,25,25,25,50,50,25,50,50,25,0},
> {25,25,50,25,25,25,100,25,25,50,0,50,50,50,50,25,25,25,0,50,0},
> {25,25,25,25,50,25,25,100,50,50,50,50,25,25,50,50,50,50,0,25,0},
> {25,0,25,50,0,25,25,50,100,25,50,50,25,50,50,25,50,25,25,25,0},
> {25,25,25,25,50,25,50,50,25,100,50,25,50,50,50,50,25,50,50,25,0},
> {25,0,0,25,25,25,0,50,50,50,100,25,25,25,50,25,50,50,25,0,0},
> {25,25,50,25,25,25,50,50,50,25,25,100,25,25,25,50,50,25,0,50,0},
> {50,25,25,25,25,25,50,25,25,50,25,25,100,50,50,50,50,25,25,25,0},
> {25,0,25,50,0,25,50,25,50,50,25,25,50,100,50,25,25,25,25,25,0},
> {25,50,25,25,25,50,50,50,50,50,50,25,50,50,100,50,50,25,50,25,0},
> {50,50,25,25,50,50,25,50,25,50,25,50,50,25,50,100,50,25,50,50,0},
> {50,25,25,25,25,25,25,50,50,25,50,50,50,25,50,50,100,25,25,25,0},
> {50,25,50,50,50,50,25,50,25,50,50,25,25,25,25,25,25,100,25,25,0},
> {25,50,0,25,25,50,0,0,25,50,25,0,25,25,50,50,25,25,100,25,0},
> {25,50,50,25,50,25,50,25,25,25,0,50,25,25,25,50,25,25,25,100,0},
> },{
> {100,9,41,50,45,73,59,54,50,54,59,45,86,54,45,54,73,68,32,45,0},
> {9,100,27,23,4,27,18,9,4,9,9,36,23,27,18,45,32,9,0,9,0},
> {41,27,100,77,18,54,59,23,50,18,27,86,50,68,54,68,59,27,14,27,0},
> {50,23,77,100,36,54,82,36,73,36,41,77,54,86,73,64,68,41,27,41,0},
> {45,4,18,36,100,27,54,86,50,86,86,27,45,45,54,27,50,77,82,86,0},
> {73,27,54,54,27,100,54,36,41,36,41,64,77,59,41,73,73,50,14,32,0},
> {59,18,59,82,54,54,100,54,82,54,59,68,64,86,86,59,77,59,45,59,0},
> {54,9,23,36,86,36,54,100,50,95,95,32,54,50,54,32,59,86,68,82,0},
> {50,4,50,73,50,41,82,50,100,50,54,54,50,73,86,41,64,54,50,59,0},
> {54,9,18,36,86,36,54,95,50,100,91,27,54,45,50,32,54,82,68,82,0},
> {59,9,27,41,86,41,59,95,54,91,100,32,59,50,54,36,59,86,68,82,0},
> {45,36,86,77,27,64,68,32,54,27,32,100,54,77,59,77,68,36,18,32,0},
> {86,23,50,54,45,77,64,54,50,54,59,54,100,64,50,64,82,68,32,50,0},
> {54,27,68,86,45,59,86,50,73,45,50,77,64,100,77,68,77,54,41,54,0},
> {45,18,54,73,54,41,86,54,86,50,54,59,50,77,100,50,64,54,50,64,0},
> {54,45,68,64,27,73,59,32,41,32,36,77,64,68,50,100,73,41,18,32,0},
> {73,32,59,68,50,73,77,59,64,54,59,68,82,77,64,73,100,68,41,54,0},
> {68,9,27,41,77,50,59,86,54,82,86,36,68,54,54,41,68,100,59,73,0},
> {32,0,14,27,82,14,45,68,50,68,68,18,32,41,50,18,41,59,100,82,0},
> {45,9,27,41,86,32,59,82,59,82,82,32,50,54,64,32,54,73,82,100,0},
> },{
> {50,25,50,75,0,25,25,0,25,0,0,25,0,50,25,25,25,0,0,0,0},
> {25,75,25,25,0,25,25,25,25,25,25,25,25,25,25,25,25,25,0,0,0},
> {25,25,75,50,0,25,25,0,25,0,0,50,25,25,25,25,25,0,0,0,0},
> {50,25,50,75,0,25,25,0,25,0,0,25,0,50,25,25,25,0,0,0,0},
> {0,0,0,0,75,0,0,50,0,25,25,0,0,0,0,0,0,25,25,50,0},
> {25,25,25,25,0,75,25,0,25,0,0,25,25,25,25,25,25,0,0,0,0},
> {25,25,25,25,0,25,75,0,25,0,0,25,25,25,25,25,25,0,0,25,0},
> {25,25,0,0,50,0,0,75,0,25,25,0,0,0,0,0,25,50,25,25,0},
> {25,25,25,25,0,25,25,0,75,0,0,50,25,25,50,25,25,0,0,0,0},
> {25,25,0,0,25,0,0,25,0,75,75,0,0,0,0,0,25,50,25,25,0},
> {25,25,0,0,25,0,0,25,0,75,75,0,0,0,0,0,25,25,25,25,0},
> {25,25,50,25,0,25,25,0,50,0,0,100,25,50,25,25,25,0,0,0,0},
> {0,25,25,0,0,25,25,0,25,0,0,25,100,25,25,25,25,0,0,0,0},
> {25,25,25,50,0,25,25,0,25,0,0,50,25,75,25,25,25,0,0,0,0},
> {25,25,25,25,0,25,25,0,50,0,0,25,25,25,75,25,25,0,25,0,0},
> {50,25,25,25,0,25,25,0,25,0,0,25,25,25,25,75,25,0,0,0,0},
> {25,25,25,25,0,25,25,25,25,25,25,25,25,25,25,25,75,25,0,0,0},
> {25,25,0,0,25,0,0,50,0,50,25,0,0,0,0,0,25,75,25,25,0},
> {0,0,0,0,25,0,0,25,0,25,25,0,0,0,25,0,0,25,75,25,0},
> {0,0,0,0,50,0,25,25,0,25,25,0,0,0,0,0,0,25,25,75,0},
> },{
> {89,11,33,44,11,33,33,22,33,22,33,33,44,33,22,44,33,33,11,11,0},
> {11,100,11,0,0,11,33,11,0,0,33,11,0,0,11,22,22,11,22,11,0},
> {33,11,89,56,11,33,44,11,33,11,22,56,33,44,11,33,33,11,0,11,0},
> {44,0,56,89,0,33,22,11,44,11,11,44,44,56,33,44,44,22,11,22,0},
> {11,0,11,0,100,0,44,33,0,56,56,0,11,0,11,22,11,33,67,67,0},
> {33,11,33,33,0,89,22,11,33,11,11,33,33,22,33,33,22,22,11,0,0},
> {33,33,44,22,44,22,89,22,44,22,33,44,33,44,56,33,44,22,33,44,0},
> {22,11,11,11,33,11,22,89,11,56,56,11,11,0,11,22,33,56,33,33,0},
> {33,0,33,44,0,33,44,11,89,22,11,44,33,44,56,33,33,22,11,11,0},
> {22,0,11,11,56,11,22,56,22,89,67,11,11,33,22,22,33,56,33,33,0},
> {33,33,22,11,56,11,33,56,11,67,89,22,11,33,11,22,33,44,11,22,0},
> {33,11,56,44,0,33,44,11,44,11,22,89,11,44,33,56,33,11,0,22,0},
> {44,0,33,44,11,33,33,11,33,11,11,11,89,33,33,33,33,22,0,0,0},
> {33,0,44,56,0,22,44,0,44,33,33,44,33,89,56,44,33,22,22,11,0},
> {22,11,11,33,11,33,56,11,56,22,11,33,33,56,89,44,33,22,33,22,0},
> {44,22,33,44,22,33,33,22,33,22,22,56,33,44,44,89,56,22,33,33,0},
> {33,22,33,44,11,22,44,33,33,33,33,33,33,33,33,56,89,33,22,11,0},
> {33,11,11,22,33,22,22,56,22,56,44,11,22,22,22,22,33,89,22,33,0},
> {11,22,0,11,67,11,33,33,11,33,11,0,0,22,33,33,22,22,100,67,0},
> {11,11,11,22,67,0,44,33,11,33,22,22,0,11,22,33,11,33,67,100,0},
> },{
> {100,72,55,53,37,82,59,47,43,47,53,67,100,63,43,90,82,65,18,37,0},
> {72,100,31,37,57,57,51,69,37,69,72,45,74,51,41,65,72,84,35,53,0},
> {55,31,100,82,18,55,67,22,61,20,27,88,53,72,55,65,61,33,4,24,0},
> {53,37,82,100,29,47,82,33,78,31,39,84,51,84,72,61,65,43,22,37,0},
> {37,57,18,29,100,20,49,88,45,88,84,27,39,45,53,33,49,72,78,92,0},
> {82,57,55,47,20,100,47,29,31,29,35,63,82,51,31,84,67,47,0,22,0},
> {59,51,67,82,49,47,100,53,84,49,57,74,59,94,84,63,74,59,39,57,0},
> {47,69,22,33,88,29,53,100,45,98,94,35,49,51,51,43,59,84,67,84,0},
> {43,37,61,78,45,31,84,45,100,41,49,65,43,80,92,47,59,47,39,53,0},
> {47,69,20,31,88,29,49,98,41,100,92,31,47,47,49,41,57,82,67,82,0},
> {53,72,27,39,84,35,57,94,49,92,100,41,55,55,55,49,65,88,63,82,0},
> {67,45,88,84,27,63,74,35,65,31,41,100,65,80,61,74,72,47,14,33,0},
> {100,74,53,51,39,82,59,49,43,47,55,65,100,63,43,90,84,65,20,39,0},
> {63,51,72,84,45,51,94,51,80,47,55,80,63,100,78,69,78,59,33,51,0},
> {43,41,55,72,53,31,84,51,92,49,55,61,43,78,100,47,61,53,47,61,0},
> {90,65,65,61,33,84,63,43,47,41,49,74,90,69,47,100,82,59,14,35,0},
> {82,72,61,65,49,67,74,59,59,57,65,72,84,78,61,82,100,72,31,53,0},
> {65,84,33,43,72,47,59,84,47,82,88,47,65,59,53,59,72,100,51,70,0},
> {18,35,4,22,78,0,39,67,39,67,63,14,20,33,47,14,31,51,100,80,0},
> {37,53,24,37,92,22,57,84,53,82,82,33,39,51,61,35,53,70,80,100,0},
> },{
> {100,64,50,57,57,43,64,50,57,64,64,50,28,64,43,57,57,50,64,50,0},
> {64,100,43,50,57,43,57,43,50,64,57,50,36,57,43,57,57,43,64,57,0},
> {50,43,100,64,14,50,50,7,64,28,21,64,43,64,57,57,50,7,28,36,0},
> {57,50,64,100,28,28,64,14,64,36,43,57,21,64,50,50,43,14,36,28,0},
> {57,57,14,28,100,36,50,71,28,64,57,28,14,36,21,43,57,64,64,57,0},
> {43,43,50,28,36,100,36,28,36,28,14,57,64,43,36,64,57,28,43,57,0},
> {64,57,50,64,50,36,100,43,64,57,57,57,21,64,57,57,57,50,57,50,0},
> {50,43,7,14,71,28,43,100,14,57,50,21,7,28,14,43,57,71,64,57,0},
> {57,50,64,64,28,36,64,14,100,36,43,64,28,71,64,57,50,21,36,36,0},
> {64,64,28,36,64,28,57,57,36,100,64,36,14,50,28,43,50,57,64,50,0},
> {64,57,21,43,57,14,57,50,43,64,100,28,0,50,28,36,43,50,57,43,0},
> {50,50,64,57,28,57,57,21,64,36,28,100,50,64,57,64,57,21,43,43,0},
> {28,36,43,21,14,64,21,7,28,14,0,50,100,36,28,57,43,7,28,43,0},
> {64,57,64,64,36,43,64,28,71,50,50,64,36,100,57,57,57,28,50,43,0},
> {43,43,57,50,21,36,57,14,64,28,28,57,28,57,100,50,50,21,36,36,0},
> {57,57,57,50,43,64,57,43,57,43,36,64,57,57,50,100,64,43,57,64,0},
> {57,57,50,43,57,57,57,57,50,50,43,57,43,57,50,64,100,57,64,64,0},
> {50,43,7,14,64,28,50,71,21,57,50,21,7,28,21,43,57,100,64,57,0},
> {64,64,28,36,64,43,57,64,36,64,57,43,28,50,36,57,64,64,100,64,0},
> {50,57,36,28,57,57,50,57,36,50,43,43,43,43,36,64,64,57,64,100,0},
> },{
> {100,8,50,88,60,60,30,88,80,78,70,78,40,90,82,95,92,95,22,50,0},
> {8,100,2,8,5,2,0,5,5,8,5,5,0,10,8,12,10,10,0,18,0},
> {50,2,100,70,38,35,12,45,48,40,32,65,15,60,42,62,45,45,10,35,0},
> {88,8,70,100,60,52,30,82,80,68,60,80,42,98,92,90,85,85,20,50,0},
> {60,5,38,60,100,35,18,70,48,70,40,55,18,62,55,58,52,65,22,95,0},
> {60,2,35,52,35,100,15,45,42,40,35,50,15,50,48,62,50,48,12,40,0},
> {30,0,12,30,18,15,100,25,20,22,15,38,5,32,35,35,22,28,2,25,0},
> {88,5,45,82,70,45,25,100,70,98,68,68,30,80,80,85,85,100,28,55,0},
> {80,5,48,80,48,42,20,70,100,62,55,70,28,88,98,80,75,75,18,58,0},
> {78,8,40,68,70,40,22,98,62,100,90,65,25,72,75,78,75,95,25,58,0},
> {70,5,32,60,40,35,15,68,55,90,100,45,15,75,72,60,65,65,12,40,0},
> {78,5,65,80,55,50,38,68,70,65,45,100,20,85,75,92,72,72,18,42,0},
> {40,0,15,42,18,15,5,30,28,25,15,20,100,30,38,38,32,30,5,15,0},
> {90,10,60,98,62,50,32,80,88,72,75,85,30,100,95,90,88,82,20,58,0},
> {82,8,42,92,55,48,35,80,98,75,72,75,38,95,100,95,92,82,25,65,0},
> {95,12,62,90,58,62,35,85,80,78,60,92,38,90,95,100,98,90,25,55,0},
> {92,10,45,85,52,50,22,85,75,75,65,72,32,88,92,98,100,85,20,52,0},
> {95,10,45,85,65,48,28,100,75,95,65,72,30,82,82,90,85,100,28,52,0},
> {22,0,10,20,22,12,2,28,18,25,12,18,5,20,25,25,20,28,100,30,0},
> {50,18,35,50,95,40,25,55,58,58,40,42,15,58,65,55,52,52,30,100,0},
> },{
> {39,29,25,27,15,29,23,23,25,21,23,25,28,26,24,32,30,27,8,15,0},
> {29,86,10,11,23,16,20,21,12,19,22,18,11,14,15,27,24,27,22,24,0},
> {25,10,51,41,4,27,29,7,29,6,11,38,23,31,25,29,27,12,0,12,0},
> {27,11,41,45,7,23,29,13,33,12,16,31,24,36,29,28,26,17,5,13,0},
> {15,23,4,7,63,0,26,32,10,37,35,11,7,13,10,12,15,27,45,53,0},
> {29,16,27,23,0,61,20,4,21,4,9,29,18,22,22,29,21,10,6,6,0},
> {23,20,29,29,26,20,58,15,30,17,20,33,21,33,30,26,25,16,23,38,0},
> {23,21,7,13,32,4,15,47,16,41,40,12,13,17,14,18,24,43,18,23,0},
> {25,12,29,33,10,21,30,16,43,16,20,31,24,34,41,27,27,18,9,16,0},
> {21,19,6,12,37,4,17,41,16,47,41,11,15,18,15,16,20,36,23,27,0},
> {23,22,11,16,35,9,20,40,20,41,49,15,14,22,18,20,24,35,22,26,0},
> {25,18,38,31,11,29,33,12,31,11,15,46,22,30,28,31,29,15,8,20,0},
> {28,11,23,24,7,18,21,13,24,15,14,22,66,26,22,29,27,18,1,11,0},
> {26,14,31,36,13,22,33,17,34,18,22,30,26,41,34,28,27,19,13,18,0},
> {24,15,25,29,10,22,30,14,41,15,18,28,22,34,51,26,26,16,18,18,0},
> {32,27,29,28,12,29,26,18,27,16,20,31,29,28,26,38,34,22,10,17,0},
> {30,24,27,26,15,21,25,24,27,20,24,29,27,27,26,34,40,27,9,17,0},
> {27,27,12,17,27,10,16,43,18,36,35,15,18,19,16,22,27,44,13,21,0},
> {8,22,0,5,45,6,23,18,9,23,22,8,1,13,18,10,9,13,100,48,0},
> {15,24,12,13,53,6,38,23,16,27,26,20,11,18,18,17,17,21,48,67,0},
> },{/*henikoff*/
> {53,27,13,20,13,27,13,20,20,20,20,13,20,20,20,33,27,27,7,13,0},
> {27,87,7,0,13,7,7,20,7,20,20,7,7,7,7,20,20,20,13,13,0},
> {13,7,67,40,7,20,20,7,20,0,7,33,20,27,13,27,20,7,0,7,0},
> {20,0,40,60,7,13,27,7,33,7,13,27,20,40,27,27,20,13,7,13,0},
> {13,13,7,7,67,7,20,27,7,27,27,7,0,7,7,13,13,20,33,47,0},
> {27,7,20,13,7,67,13,0,13,0,7,27,13,13,13,27,13,7,13,7,0},
> {13,7,20,27,20,13,80,7,20,7,13,33,13,27,27,20,13,7,13,40,0},
> {20,20,7,7,27,0,7,53,7,40,33,7,7,7,7,13,20,47,7,20,0},
> {20,7,20,33,7,13,20,7,60,13,20,27,20,33,40,27,20,13,7,13,0},
> {20,20,0,7,27,0,7,40,13,53,40,7,7,13,13,13,20,33,13,20,0},
> {20,20,7,13,27,7,13,33,20,40,60,13,13,27,20,20,20,33,20,20,0},
> {13,7,33,27,7,27,33,7,27,7,13,67,13,27,27,33,27,7,0,13,0},
> {20,7,20,20,0,13,13,7,20,7,13,13,73,20,13,20,20,13,0,7,0},
> {20,7,27,40,7,13,27,7,33,13,27,27,20,60,33,27,20,13,13,20,0},
> {20,7,13,27,7,13,27,7,40,13,20,27,13,33,60,20,20,7,7,13,0},
> {33,20,27,27,13,27,20,13,27,13,20,33,20,27,20,53,33,13,7,13,0},
> {27,20,20,20,13,13,13,20,20,20,20,27,20,20,20,33,60,27,13,13,0},
> {27,20,7,13,20,7,7,47,13,33,33,7,13,13,7,13,27,53,7,20,0},
> {7,13,0,7,33,13,13,7,7,13,20,0,0,13,7,7,13,7,100,40,0},
> {13,13,7,13,47,7,40,20,13,20,20,13,7,20,13,13,13,20,40,73,0},
> },{/*jones*/
> {35,20,25,20,10,30,15,25,20,20,20,25,30,20,20,30,35,30,5,10,0},
> {20,80,10,5,25,20,25,15,10,10,15,20,15,10,20,30,20,15,30,35,0},
> {25,10,50,45,0,30,25,10,25,5,10,35,15,30,20,25,20,15,0,15,0},
> {20,5,45,50,0,25,25,10,30,5,10,30,15,35,25,20,20,15,0,5,0},
> {10,25,0,0,65,0,25,25,0,35,25,10,10,5,5,15,15,25,20,50,0},
> {30,20,30,25,0,50,15,10,20,5,10,25,20,20,25,30,20,15,15,5,0},
> {15,25,25,25,25,15,55,10,30,15,15,30,25,35,35,20,20,10,10,45,0},
> {25,15,10,10,25,10,10,45,10,35,40,15,15,10,10,20,30,45,5,15,0},
> {20,10,25,30,0,20,30,10,50,10,15,30,15,35,45,20,20,10,10,10,0},
> {20,10,5,5,35,5,15,35,10,50,40,10,25,15,10,15,20,35,15,20,0},
> {20,15,10,10,25,10,15,40,15,40,55,15,15,15,15,20,25,35,10,15,0},
> {25,20,35,30,10,25,30,15,30,10,15,40,20,25,25,30,30,15,0,20,0},
> {30,15,15,15,10,20,25,15,15,25,15,20,55,25,20,30,30,20,5,10,0},
> {20,10,30,35,5,20,35,10,35,15,15,25,25,50,35,20,20,10,10,15,0},
> {20,20,20,25,5,25,35,10,45,10,15,25,20,35,50,20,20,10,25,15,0},
> {30,30,25,20,15,30,20,20,20,15,20,30,30,20,20,35,30,20,10,20,0},
> {35,20,20,20,15,20,20,30,20,20,25,30,30,20,20,30,35,25,5,10,0},
> {30,15,15,15,25,15,10,45,10,35,35,15,20,10,10,20,25,45,10,10,0},
> {5,30,0,0,20,15,10,5,10,15,10,0,5,10,25,10,5,10,100,25,0},
> {10,35,15,5,50,5,45,15,10,20,15,20,10,15,15,20,10,10,25,70,0},
> },{/*120pam*/
> {55,25,40,40,20,45,25,35,30,25,30,35,45,35,25,45,45,40,5,20,0},
> {25,85,5,5,10,20,20,25,5,5,10,15,20,5,20,40,25,25,0,35,0},
> {40,5,65,55,5,40,40,25,35,15,20,50,25,45,25,40,35,25,0,15,0},
> {40,5,55,65,5,35,35,25,35,20,25,45,30,50,25,35,30,25,0,15,0},
> {20,10,5,5,80,15,25,40,5,40,35,20,15,10,15,25,20,25,35,60,0},
> {45,20,40,35,15,65,20,20,25,15,20,40,30,25,20,45,35,30,0,10,0},
> {25,20,40,35,25,20,75,20,30,25,20,50,35,55,45,30,25,25,25,35,0},
> {35,25,25,25,40,20,20,70,25,45,45,30,25,25,30,30,40,55,10,30,0},
> {30,5,35,35,5,25,30,25,65,20,40,45,30,40,50,35,35,20,15,15,0},
> {25,5,15,20,40,15,25,45,20,65,55,20,25,30,20,20,25,45,25,30,0},
> {30,10,20,25,35,20,20,45,40,55,80,25,25,35,35,30,35,45,10,20,0},
> {35,15,50,45,20,40,50,30,45,20,25,60,30,40,35,45,40,25,20,30,0},
> {45,20,25,30,15,30,35,25,30,25,25,30,70,40,35,45,35,30,5,10,0},
> {35,5,45,50,10,25,55,25,40,30,35,40,40,70,45,30,30,25,10,15,0},
> {25,20,25,25,15,20,45,30,50,20,35,35,35,45,70,35,30,25,45,15,0},
> {45,40,40,35,25,45,30,30,35,20,30,45,45,30,35,55,50,30,30,25,0},
> {45,25,35,30,20,35,25,40,35,25,35,40,35,30,30,50,60,40,10,25,0},
> {40,25,25,25,25,30,25,55,20,45,45,25,30,25,25,30,40,65,0,25,0},
> {5,0,0,0,35,0,25,10,15,25,10,20,5,10,45,30,10,0,100,30,0},
> {20,35,15,15,60,10,35,30,15,30,20,30,10,15,15,25,25,25,30,80,0},
> },{
> /*
> ng-gp
> */
> {20,22,14,13,14,13,14,22,13,18,26,22,13,5,9,18,5,30,19,26,0},
> {22,0,-25,-22,7,-14,-18,-9,-5,-5,7,-18,-5,-9,-14,-14,-10,3,-33,-22,0},
> {14,-25,28,5,19,14,13,11,9,3,3,21,9,5,18,13,18,11,-2,6,0},
> {13,-22,5,19,3,10,18,11,21,15,1,13,5,9,26,5,22,18,7,22,0},
> {14,7,19,3,14,3,1,17,11,5,-3,-3,-22,-1,7,18,11,-3,12,28,0},
> {13,-14,14,10,3,19,-3,22,1,-1,-6,13,14,14,5,9,7,15,-1,-2,0},
> {14,-18,13,18,1,-3,30,7,17,-2,6,13,5,13,13,5,5,10,1,5,0},
> {22,-9,11,11,17,22,7,11,11,17,28,10,-1,-1,3,-2,5,3,-3,18,0},
> {13,-5,9,21,11,1,17,11,15,14,1,13,13,13,28,13,13,14,15,15,0},
> {18,-5,3,15,5,-1,-2,17,14,11,20,-1,9,11,-6,7,6,9,1,-7,0},
> {26,7,3,1,-3,-6,6,28,1,20,-3,1,-14,-3,3,11,14,17,9,5,0},
> {22,-18,21,13,-3,13,13,10,13,-1,1,28,5,13,18,17,9,19,-2,1,0},
> {13,-5,9,5,-22,14,5,-1,13,9,-14,5,26,6,14,13,14,14,-14,3,0},
> {5,-9,5,9,-1,14,13,-1,13,11,-3,13,6,19,21,14,13,18,3,7,0},
> {9,-14,18,26,7,5,13,3,28,-6,3,18,14,21,22,9,22,19,-7,-14,0},
> {18,-14,13,5,18,9,5,-2,13,7,11,17,13,14,9,24,17,7,-9,10,0},
> {5,-10,18,22,11,7,5,5,13,6,14,9,14,13,22,17,20,26,-16,14,0},
> {30,3,11,18,-3,15,10,3,14,9,17,19,14,18,19,7,26,7,6,26,0},
> {19,-33,-2,7,12,-1,1,-3,15,1,9,-2,-14,3,-7,-9,-16,6,5,9,0},
> {26,-22,6,22,28,-2,5,18,15,-7,5,1,3,7,-14,10,14,26,9,18,0},},};
>
>
>
> /*
> 65families
> {62,27,35,38,27,38,31,31,38,27,38,35,38,38,38,42,38,38,23,27,0},
> {27,100,0,23,27,4,12,15,19,0,8,8,0,19,27,12,12,15,12,8,0},
> {35,0,73,50,12,35,42,23,31,8,19,54,38,38,31,42,38,19,12,27,0},
> {38,23,50,69,12,35,31,23,46,15,27,42,38,50,46,35,42,31,12,31,0},
> {27,27,12,12,81,8,35,46,23,50,38,19,15,19,19,23,27,38,54,58,0},
> {38,4,35,35,8,69,27,15,27,12,23,38,35,31,31,38,27,19,19,23,0},
> {31,12,42,31,35,27,88,19,42,19,35,50,23,42,42,31,27,31,31,38,0},
> {31,15,23,23,46,15,19,73,23,50,50,27,19,12,19,23,31,54,31,35,0},
> {38,19,31,46,23,27,42,23,69,31,38,42,38,46,58,38,38,27,27,31,0},
> {27,0,8,15,50,12,19,50,31,69,58,23,27,23,23,19,23,46,38,31,0},
> {38,8,19,27,38,23,35,50,38,58,81,31,15,46,15,15,31,42,35,35,0},
> {35,8,54,42,19,38,50,27,42,23,31,69,27,38,35,46,42,15,12,35,0},
> {38,0,38,38,15,35,23,19,38,27,15,27,81,31,35,35,35,19,19,12,0},
> {38,19,38,50,19,31,42,12,46,23,46,38,31,73,50,38,38,31,15,27,0},
> {38,27,31,46,19,31,42,19,58,23,15,35,35,50,77,38,38,27,31,35,0},
> {42,12,42,35,23,38,31,23,38,19,15,46,35,38,38,62,50,27,12,31,0},
> {38,12,38,42,27,27,27,31,38,23,31,42,35,38,38,50,65,35,15,31,0},
> {38,15,19,31,38,19,31,54,27,46,42,15,19,31,27,27,35,65,15,35,0},
> {23,12,12,12,54,19,31,31,27,38,35,12,19,15,31,12,15,15,96,54,0},
> {27,8,27,31,58,23,38,35,31,31,35,35,12,27,35,31,31,35,54,81,0},
> */
>-- End of excerpt from Mark Johnson MOL

______________________________________________________________________________

On Sep 16, 11:08am, Adam Godzik wrote:
>
> Tomii K., Kanehisa M. (1996) Prot. Eng. 9:27-36
> Vogt G., Etzold T., Argos P. (1995) J. Mol. Biol. 249:816-831
>
> the web site with all the matrices - http://www.genome.ad.jp
>
> Adam
>-- End of excerpt from Adam Godzik

______________________________________________________________________________

On Sep 16, 11:48am, Adam Godzik wrote:
>
> You can find and download the indexes database by
> ftp'ing to ftp.genome.ad.jp and cd'ing to /db/genomenet/aaindex
>
>
> Adam
>-- End of excerpt from Adam Godzik

______________________________________________________________________________

On Sep 17,  3:52pm, Malcolm Cline wrote:
> Subject: homology matrices
>
> SYBYL contains six of them--Dayhoff, SwissProt, Identity, APG, Greer,
> and a physical property matrix.  If you do not have our software,
> drop me a line and I will mail copies of the matrices to you.
>
> mac
> Malcolm A. Cline
> Senior Marketing Scientist
> Tripos, Inc.
>-- End of excerpt from Malcolm Cline

______________________________________________________________________________

On Sep 17,  4:43pm, Malcolm Cline wrote:
> Subject: Re: homology matrices
>
> APG:
>
> 24
> ABCDEFHIKLMNQRSTVWYZPGX-
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>
> Note: A dash (-) represents a gap.
>
>
>
> Greer:
>
> 24
> ACDEFGHIKLMNPQRSTVWYBXZ-
> 1  0  0  0  0  .5 0  .5 0  .5 0  0  0  0  0  0  0  .5 0  0  0  0  0  0
> 0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
> 0  0  1  .5 0  0  0  0  .5 0  0  0  0  0  .5 0  0  0  0  0  1  0  .5 0
> 0  0  .5 1  0  0  0  0  .5 0  0  0  0  0  .5 0  0  0  0  0  .5 0  1  0
> 0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  .5 .5 0  0  0  0
> .5 0  0  0  0  1  0  0  0  0  0  0  .5 0  0  0  0  .5 0  0  0  0  0  0
> 0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
> .5 0  0  0  0  0  0  1  0  .5 .5 0  0  0  0  0  0  .5 0  0  0  0  0  0
> 0  0  .5 .5 0  0  0  0  1  0  0  0  0  0  .5 0  0  0  0  0  .5 0  .5 0
> .5 0  0  0  0  0  0  .5 0  1  .5 0  0  0  0  0  0  .5 0  0  0  0  0  0
> 0  0  0  0  0  0  0  .5 0  .5 1  0  0  0  0  0  0  .5 0  0  0  0  0  0
> 0  0  0  0  0  0  0  0  0  0  0  1  0  .5 0  0  0  0  0  0  1  0  .5 0
> 0  0  0  0  0  .5 0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0
> 0  0  0  0  0  0  0  0  0  0  0  .5 0  1  0  0  0  0  0  0  .5 0  1  0
> 0  0  .5 .5 0  0  0  0  .5 0  0  0  0  0  1  0  0  0  0  0  .5 0  .5 0
> 0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  .5 0  0  0  0  0  0  0
> 0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  .5 1  0  0  0  0  0  0  0
> .5 0  0  0  0  .5 0  .5 0  .5 .5 0  0  0  0  0  0  1  0  0  0  0  0  0
> 0  0  0  0  .5 0  0  0  0  0  0  0  0  0  0  0  0  0  1  .5 0  0  0  0
> 0  0  0  0  .5 0  0  0  0  0  0  0  0  0  0  0  0  0  .5 1  0  0  0  0
> 0  0  1  .5 0  0  0  0  .5 0  0  1  0  .5 .5 0  0  0  0  0  1  0  0  0
> 0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0
> 0  0  .5 1  0  0  0  0  .5 0  0  .5 0  1  .5 0  0  0  0  0  0  0  1  0
> 0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>
>
>
>
> Identity:
>
> 24
> ACDEFGHIKLMNPQRSTVWYBXZ-
>  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>
> Note: A dash (-) represents a gap.
>
>
>
>
> Physical Properties:
>
> ARNDCQEGHILKMFPSTWYVBZX-
>    1.000  -0.351  -0.166   0.085  -0.260   0.231   0.589  -0.034   0.345
  0.023
>    0.386   0.019   0.482  -0.139  -0.484  -0.104  -0.182  -0.485  -0.857
  0.126
>    0.085   0.589   0.000   0.000
>   -0.351   1.000   0.450   0.552  -0.570   0.623   0.465  -0.060   0.473
 -0.540
>   -0.583   0.813  -0.406  -0.493  -0.011   0.136   0.010  -0.234  -0.091
 -0.526
>    0.552   0.465   0.000   0.000
>   -0.166   0.450   1.000   0.866  -0.243   0.387   0.235   0.811   0.020
 -0.928
>   -0.901   0.530  -0.856  -0.845   0.500   0.788   0.215  -0.531  -0.238
 -0.854
>    0.866   0.235   0.000   0.000
>    0.085   0.552   0.866   1.000  -0.493   0.458   0.589   0.632   0.184
 -0.915
>   -0.761   0.770  -0.702  -0.850   0.312   0.575  -0.063  -0.615  -0.517
 -0.876
>    1.000   0.589   0.000   0.000
>   -0.260  -0.570  -0.243  -0.493   1.000  -0.611  -0.809   0.203  -0.589
  0.424
>    0.107  -0.776   0.035   0.311   0.179   0.169   0.376   0.253   0.424
  0.448
>   -0.493  -0.809   0.000   0.000
>    0.231   0.623   0.387   0.458  -0.611   1.000   0.592  -0.031   0.573
 -0.493
>   -0.369   0.645  -0.088  -0.571  -0.394   0.185   0.231  -0.519  -0.481
 -0.356
>    0.458   0.592   0.000   0.000
>    0.589   0.465   0.235   0.589  -0.809   0.592   1.000  -0.113   0.761
 -0.496
>   -0.080   0.768   0.102  -0.428  -0.344  -0.105  -0.459  -0.445  -0.803
 -0.483
>    0.589   1.000   0.000   0.000
>   -0.034  -0.060   0.811   0.632   0.203  -0.031  -0.113   1.000  -0.421
 -0.637
>   -0.717   0.047  -0.794  -0.707   0.632   0.893   0.388  -0.561  -0.196
 -0.525
>    0.632  -0.113   0.000   0.000
>    0.345   0.473   0.020   0.184  -0.589   0.573   0.761  -0.421   1.000
 -0.295
>    0.049   0.520   0.356  -0.139  -0.477  -0.263  -0.363  -0.129  -0.499
 -0.270
>    0.184   0.761   0.000   0.000
>    0.023  -0.540  -0.928  -0.915   0.424  -0.493  -0.496  -0.637  -0.295
  1.000
>    0.847  -0.718   0.729   0.854  -0.419  -0.662  -0.032   0.526   0.392
  0.944
>   -0.915  -0.496   0.000   0.000
>    0.386  -0.583  -0.901  -0.761   0.107  -0.369  -0.080  -0.717   0.049
  0.847
>    1.000  -0.507   0.920   0.849  -0.604  -0.842  -0.429   0.505   0.056
  0.740
>   -0.761  -0.080   0.000   0.000
>    0.019   0.813   0.530   0.770  -0.776   0.645   0.768   0.047   0.520
 -0.718
>   -0.507   1.000  -0.379  -0.571  -0.013   0.088  -0.307  -0.295  -0.393
 -0.769
>    0.770   0.768   0.000   0.000
>    0.482  -0.406  -0.856  -0.702   0.035  -0.088   0.102  -0.794   0.356
  0.729
>    0.920  -0.379   1.000   0.709  -0.782  -0.798  -0.348   0.359  -0.125
  0.687
>   -0.702   0.102   0.000   0.000
>   -0.139  -0.493  -0.845  -0.850   0.311  -0.571  -0.428  -0.707  -0.139
  0.854
>    0.849  -0.571   0.709   1.000  -0.336  -0.829  -0.409   0.858   0.544
  0.664
>   -0.850  -0.428   0.000   0.000
>   -0.484  -0.011   0.500   0.312   0.179  -0.394  -0.344   0.632  -0.477
 -0.419
>   -0.604  -0.013  -0.782  -0.336   1.000   0.629   0.234  -0.059   0.359
 -0.414
>    0.312  -0.344   0.000   0.000
>   -0.104   0.136   0.788   0.575   0.169   0.185  -0.105   0.893  -0.263
 -0.662
>   -0.842   0.088  -0.798  -0.829   0.629   1.000   0.669  -0.692  -0.181
 -0.451
>    0.575  -0.105   0.000   0.000
>   -0.182   0.010   0.215  -0.063   0.376   0.231  -0.459   0.388  -0.363
 -0.032
>   -0.429  -0.307  -0.348  -0.409   0.234   0.669   1.000  -0.481   0.118
  0.236
>   -0.063  -0.459   0.000   0.000
>   -0.485  -0.234  -0.531  -0.615   0.253  -0.519  -0.445  -0.561  -0.129
  0.526
>    0.505  -0.295   0.359   0.858  -0.059  -0.692  -0.481   1.000   0.749
  0.258
>   -0.615  -0.445   0.000   0.000
>   -0.857  -0.091  -0.238  -0.517   0.424  -0.481  -0.803  -0.196  -0.499
  0.392
>    0.056  -0.393  -0.125   0.544   0.359  -0.181   0.118   0.749   1.000
  0.252
>   -0.517  -0.803   0.000   0.000
>    0.126  -0.526  -0.854  -0.876   0.448  -0.356  -0.483  -0.525  -0.270
  0.944
>    0.740  -0.769   0.687   0.664  -0.414  -0.451   0.236   0.258   0.252
  1.000
>   -0.876  -0.483   0.000   0.000
>    0.085   0.552   0.866   1.000  -0.493   0.458   0.589   0.632   0.184
 -0.915
>   -0.761   0.770  -0.702  -0.850   0.312   0.575  -0.063  -0.615  -0.517
 -0.876
>    1.000   0.589   0.000   0.000
>    0.589   0.465   0.235   0.589  -0.809   0.592   1.000  -0.113   0.761
 -0.496
>   -0.080   0.768   0.102  -0.428  -0.344  -0.105  -0.459  -0.445  -0.803
 -0.483
>    0.589   1.000   0.000   0.000
>    0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
  0.000
>    0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
  0.000
>    0.000   0.000   0.000   0.000
>    0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
  0.000
>    0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
  0.000
>    0.000   0.000   0.000   0.000
>
>
>
>
> SwissProt:
>
> 24
> CSTPAGNDEQHRKMILVFYWBZX-
>  11.5  0.1 -0.5 -3.1  0.5 -2.0 -1.8 -3.2 -3.0 -2.4 -1.3 -2.2 -2.8 -0.9 -1.1
-1.5  0.0 -0.8 -0.5 -1.0 -3.2 -3.0  0.0  0.0
>   0.1  2.2  1.5  0.4  1.1  0.4  0.9  0.5  0.2  0.2 -0.2 -0.2  0.1 -1.4 -1.8
-2.1 -1.0 -2.8 -1.9 -3.3  0.5  0.2  0.0  0.0
>  -0.5  1.5  2.5  0.1  0.6 -1.1  0.5  0.0 -0.1  0.0 -0.3 -0.2  0.1 -0.6 -0.6
-1.3  0.0 -2.2 -1.9 -3.5  0.0 -0.1  0.0  0.0
>  -3.1  0.4  0.1  7.6  0.3 -1.6 -0.9 -0.7 -0.5 -0.2 -1.1 -0.9 -0.6 -2.4 -2.6
-2.3 -1.8 -3.8 -3.1 -5.0 -0.7 -0.5  0.0  0.0
>   0.5  1.1  0.6  0.3  2.4  0.5 -0.3 -0.3  0.0 -0.2 -0.8 -0.6 -0.4 -0.7 -0.8
-1.2  0.1 -2.3 -2.2 -3.6 -0.3  0.0  0.0  0.0
>  -2.0  0.4 -1.1 -1.6  0.5  6.6  0.4  0.1 -0.8 -1.0 -1.4 -1.0 -1.1 -3.5 -4.5
-4.4 -3.3 -5.2 -4.0 -4.0  0.1 -0.8  0.0  0.0
>  -1.8  0.9  0.5 -0.9 -0.3  0.4  3.8  2.2  0.9  0.7  1.2  0.3  0.8 -2.2 -2.8
-3.0 -2.2 -3.1 -1.4 -3.6  2.2  0.9  0.0  0.0
>  -3.2  0.5  0.0 -0.7 -0.3  0.1  2.2  4.7  2.7  0.9  0.4 -0.3  0.5 -3.0 -3.8
-4.0 -2.9 -4.5 -2.8 -5.2  4.7  2.7  0.0  0.0
>  -3.0  0.2 -0.1 -0.5  0.0 -0.8  0.9  2.7  3.6  1.7  0.4  0.4  1.2 -2.0 -2.7
-2.8 -1.9 -3.9 -2.7 -4.3  2.7  3.6  0.0  0.0
>  -2.4  0.2  0.0 -0.2 -0.2 -1.0  0.7  0.9  1.7  2.7  1.2  1.5  1.5 -1.0 -1.9
-1.6 -1.5 -2.6 -1.7 -2.7  0.9  1.7  0.0  0.0
>  -1.3 -0.2 -0.3 -1.1 -0.8 -1.4  1.2  0.4  0.4  1.2  6.0  0.6  0.6 -1.3 -2.2
-1.9 -2.0 -0.1  2.2 -0.8  0.4  0.4  0.0  0.0
>  -2.2 -0.2 -0.2 -0.9 -0.6 -1.0  0.3 -0.3  0.4  1.5  0.6  4.7  2.7 -1.7 -2.4
-2.2 -2.0 -3.2 -1.8 -1.6 -0.3  0.4  0.0  0.0
>  -2.8  0.1  0.1 -0.6 -0.4 -1.1  0.8  0.5  1.2  1.5  0.6  2.7  3.2 -1.4 -2.1
-2.1 -1.7 -3.3 -2.1 -3.5  0.5  1.2  0.0  0.0
>  -0.9 -1.4 -0.6 -2.4 -0.7 -3.5 -2.2 -3.0 -2.0 -1.0 -1.3 -1.7 -1.4  4.3  2.5
 2.8  1.6  1.6 -0.2 -1.0 -3.0 -2.0  0.0  0.0
>  -1.1 -1.8 -0.6 -2.6 -0.8 -4.5 -2.8 -3.8 -2.7 -1.9 -2.2 -2.4 -2.1  2.5  4.0
 2.8  3.1  1.0 -0.7 -1.8 -3.8 -2.7  0.0  0.0
>  -1.5 -2.1 -1.3 -2.3 -1.2 -4.4 -3.0 -4.0 -2.8 -1.6 -1.9 -2.2 -2.1  2.8  2.8
 4.0  1.8  2.0  0.0 -0.7 -4.0 -2.8  0.0  0.0
>   0.0 -1.0  0.0 -1.8  0.1 -3.3 -2.2 -2.9 -1.9 -1.5 -2.0 -2.0 -1.7  1.6  3.1
 1.8  3.4  0.1 -1.1 -2.6 -2.9 -1.9  0.0  0.0
>  -0.8 -2.8 -2.2 -3.8 -2.3 -5.2 -3.1 -4.5 -3.9 -2.6 -0.1 -3.2 -3.3  1.6  1.0
 2.0  0.1  7.0  5.1  3.6 -4.5 -3.9  0.0  0.0
>  -0.5 -1.9 -1.9 -3.1 -2.2 -4.0 -1.4 -2.8 -2.7 -1.7  2.2 -1.8 -2.1 -0.2 -0.7
 0.0 -1.1  5.1  7.8  4.1 -2.8 -2.7  0.0  0.0
>  -1.0 -3.3 -3.5 -5.0 -3.6 -4.0 -3.6 -5.2 -4.3 -2.7 -0.8 -1.6 -3.5 -1.0 -1.8
-0.7 -2.6  3.6  4.1 14.2 -5.2 -4.3  0.0  0.0
>  -3.2  0.5  0.0 -0.7 -0.3  0.1  2.2  4.7  2.7  0.9  0.4 -0.3  0.5 -3.0 -3.8
-4.0 -2.9 -4.5 -2.8 -5.2  0.0  0.0  0.0  0.0
>  -3.0  0.2 -0.1 -0.5  0.0 -0.8  0.9  2.7  3.6  1.7  0.4  0.4  1.2 -2.0 -2.7
-2.8 -1.9 -3.9 -2.7 -4.3  0.0  0.0  0.0  0.0
>   0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
>   0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
>
> Swiss Mutation Matrix
> Gaston H.Gonnet, Mark A.Cohen, Steven A. Benner,
> Exhaustive Matching of the Entire Protein Sequence Database,
> Science, 5 June 92, 256, pp. 1443-1445.
> Min =  -5.2  Max =  14.2  Ave =  -0.4
> Recommended gap penalty = 6.
>
>
>
> Since you already have Dayhoff, I am not sending it.  Hope these help!
>
> mac
>-- End of excerpt from Malcolm Cline

______________________________________________________________________________

-- 
Dimitris K. Agrafiotis, PhD              | e-mail: [email-masked]
3-Dimensional Pharmaceuticals, Inc.      | tel:    (610) 458-6045
665 Stockton Drive, Suite 104            | fax:    (610) 458-8249
Exton, PA 19341