From saarela@messi.uku.fi Wed Sep 25 05:31:21 1996 Received: from messi.uku.fi for saarela@messi.uku.fi by www.ccl.net (8.7.5/950822.1) id FAA08474; Wed, 25 Sep 1996 05:31:16 -0400 (EDT) Received: by messi.uku.fi (AIX 3.2/UCB 5.64/4.03) id AA55347; Wed, 25 Sep 1996 12:30:55 +0300 From: saarela@messi.uku.fi (Janne Saarela) Message-Id: <9609250930.AA55347@messi.uku.fi> Subject: ANNOUNCE: Plasmid Processor software available for free! To: chemistry@www.ccl.net Date: Wed, 25 Sep 1996 12:30:54 +0200 (WET) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Introduction Plasmid Processor is a simple tool for plasmid presentation for scientific and educational purposes. It features both circular and linear DNA, user defined restriction sites, genes and multiple cloning site. In addition you can manipulate plasmid by inserting and deleting fragments. Created drawings can be copied to clipboard or saved to disk for later use. Printing from withing program is also supported. Plasmid Processor is freeware, so you can use and distribute it freely. You can download full executable version of Plasmid Processor 1.02 for Windows (tm) at URL http://www.uku.fi/~kiviraum/plasmid/plasmid.html ( plasp102.zip (239k). ) Authors Plasmid Processor program was created during a programming project course organized by the Department of Computer Sciences and Applied Mathematics, University of Kuopio, Finland 1995-1996. The program was made for the Department of Biochemistry and Biotechnology, University of Kuopio, which owns the copyrights of the program. Programming team: T. Kivirauma, P. Oikari and J.Saarela. For further information please contact the authors by e-mail, plasmid@uku.fi. Any comment on program is greatly appreciated. Regards, Janne Saarela -- Janne Saarela student of BIOTECHNOLOGY, 7th grade, BSc, PhD student University of Kuopio, FINLAND Office: Room 3090, Department of Chemistry BOX 1627 FIN-70211 KUOPIO FINLAND Phone: (+358)-71-163 257 Telefax: (+358)-71-163 259 Email: saarela@messi.uku.fi WWW: http://www.uku.fi/~saarela/ Home: Mustinlammenkatu 4 B 16 FIN-70600 Kuopio FINLAND Phone: (+358)-71-2826 325 Mobile Phone: (+358)-50-68 001 From dimitris@3dp.com Wed Sep 25 10:31:23 1996 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.7.5/950822.1) id KAA09505; Wed, 25 Sep 1996 10:27:01 -0400 (EDT) Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA27809; Wed, 25 Sep 96 10:33:00 -0400 Received: by europa.3dp.com (950413.SGI.8.6.12) id KAA13621; Wed, 25 Sep 1996 10:30:47 -0400 From: "Dimitris Agrafiotis" Message-Id: <9609251030.ZM13619@europa.3dp.com> Date: Wed, 25 Sep 1996 10:30:46 -0400 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Su: amino acid exchange matrices Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii 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: mark@hops.btk.utu.fi > * > */ > > References: > > Johnson, M.S. & Overington, J.P. (1993). > "A structural basis for the comparison of sequences: An > evaluation of scoring methodologies." J. Mol. Biol. 233, 716-738. >

> Johnson, M.S., Overington, J.P. & Blundell, T.L. (1993). > "Alignment and Searching for Common Folds Using a Data Bank of Structural > Templates." > J. Mol. Biol., 231, 735-752. >

> 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," > Methods in Enzymology 266, 575-598. >

> 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." > Proc. 27th Hawaii Intern. Conf. Syst. Sci. V, 296-305. >

> 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." > Protein Science 1, 216-226. >

> Overington, J.P., Johnson, M.S., \(vSali, A. & Blundell, T.L. (1990). > "Tertiary constraints on protein evolutionary diversity: Templates, > key residues and structural prediction." > Proc. Roy. Soc. London B 241,132-145. >

> 
> /* 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
> ##
> ##  	jpo@sandwich.pfizer.com
> ##
> ##	Dr. Mark Johnson
> ##	Turku Center for Biotechnology
> ##	University of Turku & Abo Akademi University
> ##	PO Box 123
> ##	FIN-20521 Turku, Finland
> ##
> ##	mark@hops.btk.utu.fi
> ##
> ## 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: dimitris@3dp.com
3-Dimensional Pharmaceuticals, Inc.      | tel:    (610) 458-6045
665 Stockton Drive, Suite 104            | fax:    (610) 458-8249
Exton, PA 19341


From owner-chemistry@ccl.net  Wed Sep 25 14:00:28 1996
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From: "Emadeddin Tajkhorshid" 
Message-Id: <9609251845.ZM11163@mbp-sgi7.inet.dkfz-heidelberg.de>
Date: Wed, 25 Sep 1996 18:45:12 +0100
Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de
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Subject: Freezing a number of atoms in G94
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Dear CCLers

I want to know if it is possible to freeze a number of atoms in their cartesian
coordinates during G94 geometry optimization.

many thanx

-- 
Emad
*********************************************************************
E. Tajkhorshid				
German Cancer Research Center; DKFZ  Tel: +49 6221 42 2339
Dept. Molecular Biophysics (0810)    FAX: +49 6221 42 2333
P.O.Box 101949			   Email: E.Tajkhorshid@DKFZ-Heidelberg.DE
69009 Heidelberg, FRG
***********************************************************************
* A friend may well be reckoned a masterpiece of the nature (Emerson) *
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From owner-chemistry@ccl.net  Wed Sep 25 15:00:18 1996
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From: "Stephen R. Heller" 
To: jcicshelp , chemistry@ccl.net,
        chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu
Cc: ken@softshell.com, "Stephen R. Heller" 
Subject: Software for Review
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Subject: Software and Database for Review

September 25, 1996

Subject:  Computer Software for Review

     As the Software Review Editor for the ACS Journal of
Chemical Information and Computer Science (JCICS) I often get
software for review in the journal.   I have 2 new software and
database products. I am looking for people who are willing to
review these software/databases products.  In return for the
review which is published in JCICS you get to keep the software
or database.  The review should be completed in 1-3 months.  The
length of the review is 4-10 double spaced typed pages.  Sample
reviews can be found in most of the recent issues of JCICS.

     Please try to give me some (short) reason to choose you over
another person. DO NOT SAY YOU WILL REVIEW ANYTHING I HAVE
AVAILABLE.  Messages with such replies are trashed!

     I have tried this approach for about the past five years and
it is working reasonably well. (REMINDER: For those who haven't
finished your reviews of software sent months and months ago,
this last sentence does not apply to you!)  As a result, I am
continuing this new method to find reviewers using this e-
mail/user group system.  I reserve the right to abandon this if
it is a problem, or inappropriate.  I will not notify people if I
have found a reviewer.  If you don't hear from me within a few
days I have chosen someone else to review the particular package.

     As I get many, many, (too many) replies to this message,
please do not respond after 26 September 1995 (Thursday), as I am
sure the software will be gone by then.

     I can be reached on Internet (SRHELLER@GIG.US.GOV).

     PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX
NUMBER!!!  (I send the software by Federal Express.)  Without
this information I WILL NOT consider your request.


     Steve Heller


The packages I now have are:

1. Chemwindows DB 4.0, a chemical structure drawing program from
Softshell.  For Windows 95/NT only.

2. SymApps 1.0, a program to calculate and display symmetry point
groups.  Also used for visualization (4 different styles)and high-
quality publishing.  For Windows 95/NT only.

Steve Heller, USDA, ARS, Plant Genome Project
Bldg. 005, Room 337
Beltsville, MD 20705-2350 USA
Phone: 301-504-6055   FAX: 301-504-6231
E-mail:  srheller@gig.usda.gov
WWW:     www.hellers.com/~steve