Off topic:Problems with entering a sequence on Pfscan (Prosite)

Question

[bzamith26]

Dear all,

I was wondering if you could help me to solve a problem.

I've downloaded ps_scan_linux_x86_elf.tar.gz from ftp://ftp.expasy.org/databases/prosite/ps_scan/ and unpacked it. I am using Linux Mint.

All I want to know is how to input my sequences, that are on fasta format.

When I type

~/Downloads/ps_scan $ ./pfscan

I receive this message, which I will call "message 1":

pfscan 2.3 revision 4
Usage: pfscan[ -abCdfhlLmMkrsuvWxyz ] [ seq-file | - ] [ profile-library-file | - ] [ parameters ]

   options:
    -a: report optimal alignment for all profiles.
    -b: search complementary strand of DNA sequences.
    -f: input sequence file is in FASTA format.
    -h: print usage help text.
    -l: indicate highest cut-off level (number).
    -L: indicate highest cut-off level (text).
    -m: report individual matches for circular profiles.
    -r: use raw score.
    -u: force profile disjointness to UNIQUE.
    -C<value>:
        cut-off level to be used for match selection. Same as parameter L.
    -M<value>:
        set the normalization mode to use for the score computation.
        Overrides the profile PRIORITY parameter.

   output modifiers:
    -d: impose length limit on profile description.
    -k: output using the xPSA header (using keyword=value pairs).
    -s: list sequences of the matched regions.
    -v: suppress warnings on stderr.
    -x: list alignments in PSA format.
    -y: list alignments in human readable form.
    -z: indicate profile start and stop positions.
    -W<value>:
        specifies the output width. Same as parameter W.

   valid (but deprecated) parameters are:
    [L=cut-off-level]  use option -C instead
    [W=output-width]   use option -W instead

So, when I try:

~/Downloads/ps_scan $ ./pfscan -flxz seq.fasta

I keep receiving the same 'message 1', with no differences.

Also tried:

~/Downloads/ps_scan $ perl ./ps_scan.pl -fs seq.fasta

And I got:

Cannot open seq.fasta

When I try:

~/Downloads/ps_scan $ ./pfscan -flxz -v seq.fasta L=-1

as shown here (ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pft2.3/documentation/pfscan.1.html),

I get:

Error: Unable to open sequence file 'seq.fasta'.

P.S: The sequence file is on the same directory/folder of pfscan (/Downloads/ps_scan).

P.S2: I've downloaded prosite.dat too and it is on the same directory/folder of pfscan (/Downloads/ps_scan)

What can I do to solve this problem?

I've already tried running the sequences on online prosite tool and everything worked pretty well.

Best regards,
Bruna Zamith
Freshman on Bioinformatics area