Index of /downloads/scanps1

Name	Last modified	Size

Parent Directory		-
owl_29.3.tar.gz	1998-08-10 18:10	33M
scanps_1.0.tar.gz	1998-08-10 18:11	1.6M
scanps_1.01.tar.gz	1998-08-10 18:11	1.6M

Announcing SCANPS
-----------------

Geoffrey J. Barton

Lab of Molecular Biophysics
Rex Richards Building 
South Parks Road
Oxford OX1 3QU
UK.

gjb@bioch.ox.ac.uk

UPDATE: 13/8/1997

Version 1.01 - recompiled for Silicon Graphics IRIX 6.2 and R10K processor.
Otherwise similar to Version 1.0.
Note:  Comparison of speed with SSEARCH was done with an earlier version
of SSEARCH than that distributed today (13/8/1997).

----------------

SCANPS (pronounced Scan-P-S) stands for SCAN Protein Sequence.  The
main function of SCANPS is to use a rigorous local alignment method to
search protein sequence databases with a query sequence or multiple
alignment.  SCANPS also allows all pairwise comparsons to be made
between a set of sequences and can estimate the statistical
significance of the alignments.  SCANPS has been used in the analysis
of many protein families.  For example, it was used to make the
discovery of similarity between PD-ECGF (Platelet derived endothelial
cell growth factor) and TP (Thymidine Phosphorylase) (Barton, 1992).
The program was also used to find the similarity between E. coli
diadenosine tetra-phosphatase and the protein Ser/Thr phosphatases
(Barton, et al, 1994).

Principal features of SCANPS
----------------------------

Efficient finding of Nearly-ALL local alignments (the NALL method)
(Barton, 1993) that score above a cutoff or probability threshold,
between a sequence and a database.  This means if two proteins have
more than one common region, most regions are reported.  Effectively,
this is like BLAST (Altschul et al, 1990) but with gapped alignments.

Efficient implementation of the Smith-Waterman Algorithm - this
returns the highest scoring local alignment between two sequences
including gaps where necessary.  The program is approximately a factor
of three faster than sssearch.

Estimation of the significance of the local alignments.  An empirical
method is used which takes into account the alignment score and the
alignment length.  This has the effect of pushing unusually high
scoring, but short alignments higher up the hit list.

Comparison of all pairs of sequences in a set using either the
Smith-Waterman, or NALL methods.

Availability
------------

The SCANPS program has been used as a test bed for a lot of studies,
many of which are not yet published.  When the work is published, I
will try to clean up the source code and distribute it.  Currently, I
can not be sure that the code will compile on all ANSI-C compilers, so
for the time being, I am making precompiled binaries available for Sun
(SunOS 4.1.3) and Silicon Graphics (IRIX 5.2).  I have access to a Silicon
Graphics running IRIX 4.X, so if you want the programs on the older operating
system, then let me know.

The programs are available by anonymous ftp from geoff.biop.ox.ac.uk
in the subdirectory programs/scanps.  You can also reach this
directory using a WWW browser such as Mosaic
(URL=http://geoff.biop.ox.ac.uk).   You can also read preprints of 
related papers on line at this site, or download PostScript copies.

If you download the programs please send me a short email with your
name, affiliation and address.  I will add you to my user database and
send you an email when the programs are updated and/or sources are
made available.


References
----------

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman.
J. Mol. Biol., 215:403-410, 1990.

G. J. Barton.
Comput. Appl. Biosci., 9:729-734, 1993.

G. J. Barton, P. T. C. Cohen, and D. Barford.
Eur. J. Biochem., 220:225-237, 1994.

G. J. Barton, C. P. Ponting, G. Spraggon, C. Finnis, and D. Sleep.
Protein Science, 1:688-690, 1992.
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This directory contains the SCANPS distribution in the file
scanps_1.0.tar.gz.

It also contains the pir sequence database complete with indexes
for the scanps program "sortsco".  This database expands to 
about 30 megabytes.

You need the GNU gunzip program to uncompress these distribtions - 
please see an ftp site near you!

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