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!
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written
by
kiminsigne •
3 answers
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.
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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Are you certain the script is in your path or in your working directory? The script should generate a help message with no arguments.