PrattWWW

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 are ready:

• 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

1. 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.
2. 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.

1. 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.
2. 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 window).