boxshade 2.7 released

Lee F. FrankKolakowski lfk at receptor.mgh.harvard.edu
Wed May 25 13:12:50 EST 1994

I apologize for the post lacking any new info.

On 25 May 1994 09:31:28 -0700,
helgew at LJCRF.EDU (Helge Weissig) said:
>>The new version (2.7) is for users of DOS, VMS and OSF1 machines.
OSF1 is a version of Unix.

> Is there anything comparable available for Unix or Mac systems?

I, my self am a fan of ALSCRIPT.  Alscript and a package of other
programs are available from Geoff Barton.

Here is the blurb.

From: gjb at bioch.ox.ac.uk (Geoff Barton)
Subject: Software Available
Keywords: protein structure, sequence alignment
Organization: Department of Biochemistry, University of Oxford
Date: Thu, 27 Jan 1994 17:10:39 GMT


1st Announcement  27 January 1994

From:     Geoff. Barton      gjb at bioch.ox.ac.uk
	  Craig Livingstone  cdl at bioch.ox.ac.uk
	  Rob. Russell       rbr at bioch.ox.ac.uk

University of Oxford
Laboratory of Molecular Biophysics
Rex Richards Building
South Parks Road
Oxford OX1 3QU

Tel: (44) 865 275368   (direct)
Fax: (44) 865 510454

The following packages are now available for academic, teaching and
non-commercial purposes.  For commercial use, a commercial licence is
required - please contact G. J. Barton for details.

All packages include full source code, example files and documentation.

alscript	Program to take a multiple protein sequence alignment
		and "prettify" it.  Boxing, shading, font changes etc.
		(Language - ANSI-C, Runs on most Unix computers + VMS 
		+ MS-DOS). 

   		Barton, G. J. (1993)
   		ALSCRIPT a tool to format multiple sequence alignments
   		Protein Engineering, Volume 6, No. 1, pp.37-40.

amps		Multiple protein sequence alignment and flexible pattern
		matching programs.  These do "normal" multiple alignment
		but also include features to make use of additional non
		sequence information (e.g. secondary structures) when 
		this is available. (Language: Fortran 77 and C - known to 
		run on Sun and SGI, partial implementation under VMS).

		Barton, G. J. (1990), [Review]
	    	"Protein Multiple Sequence Alignment and Flexible 
		Pattern Matching",  Meth. Enzymol., 183, 403-428.

		Barton, G. J. and Sternberg, (1987),
    		"A Strategy for the Rapid Multiple Alignment of 
		Protein Sequences:  Confidence Levels From Tertiary 
		Structure Comparisons",	 J. Mol. Biol., 198, 327-337.

amas		Automatic analysis of multiple protein sequence alignments.
		Identifies the most interesting features of an alignment
		and provides a text summary and boxed/shaded/coloured 
		alignment.  (Language - C, Sun, SGI, ALPHA/VMS probably others)

		Livingstone, C. D. and Barton, G. J. (1993), 
		"Protein Sequence alignments: a strategy for the hierarchical
		analysis of residue conservation", CABIOS, 9, 745-756.

stamp		Alignment of multiple protein structures.  Database scanning
		with a 3D structure.  NOTE this package deals with 
		3D structures NOT sequences, but a sequence alignment is
		one result.  (Language C and Fortran. Sun, SGI).

		Russell, R. B. and Barton, G. J. (1992),
	    	"Multiple protein sequence alignment from tertiary structure 
     		comparison:  assignment of global and residue confidence 
		levels", Proteins, 14, 309-323.

		Russell, R. B. and Barton, G. J. (1993),
		"An SH2-SH3 Domain hybrid", Nature, 364, 765.

assp		Takes a multiple sequence alignment and estimates the
		lower limit in accuracy one should expect for a 
		perfect consensus secondary structure prediction based on the
		alignment.  (Language - C, Sun, SGI).

		Russell, R. B. and Barton, G. J. (1993),
		J. Mol. Biol., 234, 951-957,
		"The Limits of Protein Structure Prediction Accuracy 
		From Multiple Sequence Alignment"


1. Log into our anonymous ftp server : geoff.biop.ox.ac.uk

2. Download the file README.         

3. Follow the instructions therein.

Frank Kolakowski

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