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Next: Building SCANPS Databases Up: Installing SCANPS Previous: Computer requirements

Step-by-step installation

  1. Unpack the scanps distribution into a directory. Assuming we do this in /usr/local then:

    tar zxf scanps_2.3.9.tar.gz
    

    will create a directory structure like this:

    /usr/local/scanps_2.3.9
    /usr/local/scanps_2.3.9/doc      (Documentation)
    /usr/local/scanps_2.3.9/bin      (Executables for scanps)
    /usr/local/scanps_2.3.9/dat      (Configuration and data files for scanps)
    /usr/local/scanps_2.3.9/mat      (Pairscore matrix files - e.g. BLOSUM)
    /usr/local/scanps_2.3.9/examples (Example output discussed in manual)
    /usr/local/scanps_2.3.9/db       (Example swissprot database files)
    

    the binary directory contains a README file that explains what the different binaries are for. You should provide a link from your normal bin directory to the appropriate binary for your system. For example if you normally put local binaries in /usr/local/bin:

    cd /usr/local/bin
    ln -s /usr/local/scanps_2.3.9/bin/xpscanps_16K scanps
    

    will put the standard MMX and SSE scanps for Linux in your path.

  2. Configure the dat/scanps_defaults.dat file. Find the following lines in the file:

    MATRIX_DIR  /usr/local/scanps/mat/
    GENERAL_DIR /usr/local/scanps/dat/
    DB_DIR      /usr/local/scanps/db/
    

    edit the lines MATRIX_DIR and GENERAL_DIR to specify the ``mat'' and ``dat'' subdirectories of the scanps distribution. edit the DB_DIR line to point at the directory where you will put scanps database files that you will search against. There is an example SWISS-PROT database in the directory scanps/db for testing, but you should build your own databases before using scanps for real scans. For speed, the database directory should be on a disk local to to the computer on which you will run scanps.

  3. Set the SCANPSDIR environment variable to point at the scanps/dat directory. If you use the c-shell then type:

    setenv SCANPSDIR /usr/local/scanps/dat/
    

    if you use the bash shell, then do:

    set SCANPSDIR=/usr/local/scanps/dat/
    

  4. Type /usr/local/bin/scanps (or whatever the path to scanps is that you have defined) and you should see something like:

    /usr/local/bin/scanps
    ---------------------------------------------------------------------
    SCANPS Version: 2.3.9 (Wed Jul 17 14:02:27 BST 2002)
    Authors: GJ Barton, SMJ Searle, C. Webber:  University of Dundee and EMBL-EBI
    ---------------------------------------------------------------------
    See scanps_manual for FULL information.
    Normal scans:
    MODE  200:  Protein vs protein with iteration and simple gaps.
    MODE  202:  Protein vs protein with iteration and affine gaps.
    
    Experimental methods:
    MODE  210:  Protein vs protein with iteration and variable simple gaps.
    MODE  212:  Protein vs protein with iteration and variable affine gaps.
    
    MODE 99:  Build a scanps database - see scanps_manual.
    
    Assuming SCANPS has been installed correctly, the following should work...
    
    MODE 200 scan with FASTA format file query.seq against SwissProt
    scanps -s query.seq -qseq_format 1 -bdb swissprot > logfile
    
    To scan a fasta format database in any mode change -bdb swissprot to:
    -d swissprot.fa -db_format 1
    
    Common options - for full list, see scanps_manual
    Change pairscore matrix from default to another matrix, e.g. PAM100
    Add:  -m PAM100 to command line
    Change gap penalties - e.g. to length dependent of 9 and creation of 13 
    Add:  -ugd 0 -ld_pen 9 -li_pen 13
    
    ---------------------------------------------------------------------
    SCANPS Version: 2.3.9 (Wed Jul 17 14:02:27 BST 2002)
    Authors: GJ Barton, SMJ Searle, C. Webber:  University of Dundee and EMBL-EBI 
    ---------------------------------------------------------------------
    

    Assuming you have set the DB_DIR line in scanps/dat/scanps_defaults.dat to point at the scanps/db directory, then you should now be able to run a test of SCANPS.

    cd /usr/local/scanps/examples  (or wherever you have put scanps)
    /usr/local/bin/scanps -s test.fa -bdb sprot > mytest.log
    

    This will take all the default values for a search, output options etc and put the results in the file `mytest.log'. You can look at this output file and compare it to the file `test.log' in the same directory. As a quick check of your SCANPS installation, you can `diff' the two files There should only be minor differences similar to those shown below:

    cd /usr/local/scanps/examples
    diff test.log mytest.log
    1c1
    < # SCANPS Scan:    Tue Jul 23 10:43:05 2002
    ---
    > # SCANPS Scan:    Tue Jul 23 10:14:46 2002
    1283c1283
    < # Scan Completed at: Tue Jul 23 10:43:05 2002
    ---
    > # Scan Completed at: Tue Jul 23 10:14:47 2002
    1287,1291c1287,1291
    < # Load database:                       0.6     0.6     0.7     0.7
    < # Scan database:                       9.3     9.9     9.3    10.0
    < # Output scores:                       0.5    10.3     0.5    10.4
    < # Generate and write alignments:       0.3    10.7     0.3    10.8
    < # Millions of cell updates/sec in scan (CPU): 323.68 (Elapsed): 323.68
    ---
    > # Load database:                       1.2     1.2     3.5     3.5
    > # Scan database:                       9.7    10.8    10.8    14.3
    > # Output scores:                       0.8    11.6     1.0    15.3
    > # Generate and write alignments:       0.4    12.0     0.6    15.9
    > # Millions of cell updates/sec in scan (CPU): 310.33 (Elapsed): 278.72
    

If you get the above output or similar, then all is happiness. Now lets go through some of the different scanps options, examine the output in more detail and how to control what you see in the output file.


next up previous
Next: Building SCANPS Databases Up: Installing SCANPS Previous: Computer requirements
Geoff Barton (GJB) 2002-07-23