next up previous
Next: Obtaining more than one Up: Standard SCANPS search Previous: Multiple Alignment Output


This is just some timing information at the moment - this can be useful to diagnose performance problems on a computer.

# Scan Completed at: Tue Jul 23 10:14:47 2002
# Times:                              (Seconds)
# Load matrix, query and index:        0.0     0.0     0.0     0.0
# 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

The above times were obtained on a 1GHz PIII processor for the test.fa sequence against sprot. The important numbers to look at when making comparisons are the first column and the last row. For example, the time taken to scan the database was 9.7 seconds, which corresponds to 310 Million Cell updates/second. If you see big numbers by the ``Load database'' row, then you have a disk access problem or you do not have enough RAM to store the database. On most machines the swissprot database should load in under 2 seconds.

Geoff Barton (GJB) 2002-07-23