Uppsala Software Factory - SBIN
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Manuals
- STRUPRO to generate PROSITE-formatted
profiles from a set of superimposed 3D protein structures
- ZPROF to calculate Z-scores
from the results of a profile/database scan
- PRF2MSEQ to convert the results
of a profile/database scan into a partial multiple sequence
alignment, suitable as input to MSEQPRO
- MSEQPRO to generate PROSITE-formatted
profiles from a set of aligned protein sequences
- STRUPAT to generate PROSITE
patterns from a set of superimposed 3D protein structures
- MSEQ2ALSC to convert multiple
sequence alignment files from STRUPRO or PRF2MSEQ into input
files for ALSCRIPT.
(Example PostScript file from STRUPRO,
MSEQ2ALSC, ALSCRIPT)
(Example PostScript file from PRF2MSEQ,
MSEQ2ALSC, ALSCRIPT)
Description
SBIN is a set of "structural bioinformatics" programs for sequence
pattern and profile analysis. An
introduction to the package
is available.
SBIN is a suite of "structural bioinformatics" programs. SBIN
operates at the interface of structural biology and the world of protein
sequences. Its major purpose is to help structural biologists to use the
results of their structural studies in order to detect other proteins which may
be related in structure and/or function. The package contains the following
programs:
- STRUPAT - a program which reads multiple aligned protein structures
(in PDB format; the structures must have been superimposed previously,
e.g. using LSQMAN of the DEJAVU package) and produces a
set of PROSITE-style sequence patterns (a.k.a. footprints, fingerprints or
motifs). These in turn can be used to scan the SWISSPROT and TREMBL databases
(e.g., at http://www.expasy.ch/sprot/scnpsit2.html) to find other
protein sequences which match the pattern (and might therefore be related in
structure and/or function).
- STRUPRO - this program is similar to STRUPAT, but instead of
patterns it generates sequence profiles, which tend to be superior to patterns.
The profiles can be scanned against a local sequence database (e.g.,
SWISSPROT from ftp://ftp.expasy.ch/databases/swiss-prot/) with the "pftools"
package of Philippe Bucher (mailto:pbucher@isrec-sun1.unil.ch), available from
http://ulrec3.unil.ch:80/ftp-server/pftools/.
- MSEQ2PRF - the results of a profile-database scan can be used to
iteratively refine the profile. MSEQ2PRF will produce a
multiple-sequence alignment from scan results.
- MSEQPRO - this program does the same as STRUPRO, but instead of
aligned 3D structures, it uses a multiple-sequence alignment as input to
generate a profile.
- ZPROF - this programs takes the result of a profile scan against an
entire sequence database in order to derive the average score and its standard
deviation, which enables one to calculate Z-scores.
- MSEQ2ALSC - this converts a multiple-sequence alignment (as produced
by STRUPRO and MSEQ2PRF) into an input file for Geoff Barton's
ALSCRIPT program.
Platforms
SBIN is available for SGI and DEC ALPHA/OSF1 workstations. For profile
analysis, a local copy of the SWISSPROT database and the "pftools" package is
required (see above).
References
- GJ Kleywegt & TA Jones, Acta Cryst.,
D54, 1119-1131 (1998).
Latest update at 6 February, 1999.
