Cannot get local ps_scan.pl to run

Question

[kiminsigne]

I'm trying to run ps_scan.pl locally (downloaded from the ScanProsite website) but I can't get the script to run.

I'm typing the command:

perl ps_scan.pl input.fasta

as shown in the documentation, but the program just returns with no output. Any insights as to where I'm going wrong? Thanks so much!

[SES]

Are you certain the script is in your path or in your working directory? The script should generate a help message with no arguments.

Answer 1

[Elisabeth Gasteiger]

If you have not been able to get this to run, please don't hesitate to contact the ExPASy helpdesk ([e-mail]) with an example input file, and specify which operating system you are using.

Answer 2

[MAPK]

Try running it as

./ps_scan.pl input.fasta

Answer 3

[hpmcwill]

Assuming that ps_scan.pl has been configured (the appropriate paths set for the binaries and data files), I suspect the reason may be simply that your sequence has not matches against the default settings.

See Local Copy Of Scan Prosite Not Returning Good Results for a discussion of using ps_scan.pl and scanning both patterns and profiles from the PROSITE database.

For comparison you may want to test your sequences with the online services based on ps_scan.pl:

• ScanProsite
• PROSITE Scan

As Elisabeth notes, if you still have problems with the software you can contact the developers via the ExPASy helpdesk.