Oxford Protein Software
Oxford Protein Software
home
software section
1st Announcement 27 January 1994
>From: Geoff. Barton gjb@bioch.ox.ac.uk
Craig Livingstone cdl@bioch.ox.ac.uk
Rob. Russell rbr@bioch.ox.ac.uk
University of Oxford
Laboratory of Molecular Biophysics
Rex Richards Building
South Parks Road
Oxford OX1 3QU
UK.
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"
---------------------------------------------------------
HOW TO OBTAIN THE PROGRAMS:
--------------------------
1. Log into our anonymous ftp server : geoff.biop.ox.ac.uk
2. Download the file README.
3. Follow the instructions therein.
Recover the files by anonymous ftp.
Please send your comments and your suggestions to Yves Epelboin, epelboin@lmcp.jussieu.fr .
