The PrattWWW server allows the user to use Pratt on-line.
He/she can input his/her own sequence data, and set some parameters
to control the pratt search for conserved patterns.
Pratt is automatically started at a machine in Bergen.
In order to keep the load on this machine down, we have
limited the time to be used by Pratt to maximum one minute.
The results from Pratt is shown on a new WWW page once they
- The plain text output file produced by Pratt is shown, and
- Java applet PatSeq gives a graphical representation
of the position of the patterns in the input sequences.
Alternatively, the user can input an output file from Pratt
which has been produced earlier (for instance using the user's
locally installed Pratt). This output file should be an unmodified
output file from Pratt v2.1 run with -WWW as a command line parameter.
When this option is on, Pratt will output the sequence lengths to the output
file (which are needed by the PatSeq applet).
For the Pratt parameters, and explanation of what these means
we refer to the Pratt Documentation page.
The Java applet PatSeq shows
PatSeq allows for some interactivity:
- The pattern list:
The patterns discovered by Pratt in PROSITE pattern notation
- each pattern is also given a unique graphical representation.
Rectangles and ellipses in 10 different colours give 20 different
combinations, and therefore the limit of patterns that can
be visualised using PatSeq is 20.
- The sequences with pattern matches:
The sequences are shown - for each sequence a line is drawn with a length
proportional to the sequence length, and for each pattern match in the sequence,
the graphical representation for the pattern is shown on top of the line
representing the sequence in a position defined by the segment in the sequence
matching the pattern.
- The user can by clicking on the pattern symbols in the pattern list, switch
on and off patterns, the patterns matches in the sequences are only shown for
patterns that are switched on.
- By clicking on a pattern symbol in a sequence, some information about
this particular pattern is shown on the status line (at the bottom of the WWW-browser