Cannot get local ps_scan.pl to run
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7.5 years ago
kiminsigne • 0

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!

prosite • 1.7k views
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Are you certain the script is in your path or in your working directory? The script should generate a help message with no arguments.

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7.5 years ago

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

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7.5 years ago
MAPK ★ 1.9k

Try running it as

./ps_scan.pl input.fasta

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7.5 years ago
hpmcwill ★ 1.2k

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:

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

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