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Problems with entering a sequence on Pfscan (Prosite)

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

pfscan prosite input sequence fasta
• 2,523 views • link
updated by Ram Ram • written by bzamith26 • bzamith26

Quick question: The -l option seems to be looking for a numerical input for the threshold value. Any reason you're not giving it one in your command?

• 0 views • link
written by Ram Ram

Hello bzamith26!

We believe that this post does not fit the main topic of this site.

OP asked "wrong question". See Problems running ps_scan.pl

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
written by Ram Ram

2 answers

Hi Bruna,

pfscan is for scanning motifs against protein sequences, both of which must be supplied by the user (i.e. you).

message1 is the help/usage message. It gets displayed when you call the program without any arguments, with argument -h or when arguments are wrong in one way or another.

  • ./pfscan => help message, normal because no arguments was supplied
  • ./pfscan -flxz seq.fasta => can't work because the profile file is missing

Try something like:

pfscan -f 'seq.fasta' 'profile.txt'

The -f is to specify that your input sequence file is in fasta format.

For testing follow these steps:

  • Go to the directory where you want to put your test sequence
  • Do: 'wget http://www.uniprot.org/uniprot/P24664.fasta'
  • Go to the directory where you want to put your test profile
  • Do: wget http://prosite.expasy.org/PS50240.txt
  • Go to the directory containing pfscan
  • $path_to_pfscan/pfscan -f $path_to_your_sq/P24664.fasta $path_to_your_prf/PS50240.txt

There you should get a result.

p.s. To Ram: I'm not sure how the level param works, I used the -l without giving a number and it didn't complain, it just stated the level that was used.

Kind Regards,
Béatrice

• 0 views • link
updated by Ram Ram • written by beatrice.cuche • beatrice.cuche

I'm guessing the tool may have been designed to get() when -l is passed without a parameter and set() when a parameter is given. You may wish to check what happens when you give it a parameter. A better solution would be to look at the input processing code if the tool is open source.

• 0 views • link
written by Ram Ram

By default pfscan reports matches at the cut-off level=0, if we take PS50240:

....
MA   /CUT_OFF: LEVEL=0; SCORE=1134; N_SCORE=9.5; H_SCORE=34749; MODE=1; TEXT='!';
MA   /CUT_OFF: LEVEL=-1; SCORE=775; N_SCORE=6.5; H_SCORE=27986; MODE=1; TEXT='?';
...

it means that by default. if a protein match scores above 6.5 but below 9.5 it won't be shown. To display it we need to tell pfscan to perform the run at level -1 .

It looks like both -l and -L parameters just show the cut-off level at which a protein sequence is matched, To run the scan at a different cut-off than level = 0, -C must be used followed by the level see examples below:

P24664 scanned against PS50240 with a score of 30.624 (i.e. above cut-off at level=0)

pfscan  -f P24664.fasta PS50240.txt
  30.624   3660 pos.        1 -     223 PS50240|TRYPSIN_DOM Serine proteases, trypsin domain profile.
pfscan  -fl P24664.fasta PS50240.txt
L=0   30.624   3660 pos.        1 -     223 PS50240|TRYPSIN_DOM Serine proteases, trypsin domain profile.
pfscan  -fL P24664.fasta PS50240.txt
!   30.624   3660 pos.        1 -     223 PS50240|TRYPSIN_DOM Serine proteases, trypsin domain profile.

Q5WTI5 scanned against PS50240 with a score of 30.624 (i.e. below cut-off at level=0 and above the one at level=-1)

pfscan  -f Q5WTI5.fasta PS50240.txt
No Results
pfscan  -fl Q5WTI5.fasta PS50240.txt
No Results
pfscan  -fL Q5WTI5.fasta PS50240.txt
No Results
pfscan  -f -l -1 Q5WTI5.fasta PS50240.txt
No Results
pfscan  -f -L -1 Q5WTI5.fasta PS50240.txt
No Results
pfscan  -f -C -1  Q5WTI5.fasta PS50240.txt
   6.506    776 pos.       97 -     318 PS50240|TRYPSIN_DOM Serine proteases, trypsin domain profile.
pfscan  -f -l -C -1  Q5WTI5.fasta PS50240.txt
L=-1   6.506    776 pos.       97 -     318 PS50240|TRYPSIN_DOM Serine proteases, trypsin domain profile.
pfscan  -f -L -C -1  Q5WTI5.fasta PS50240.txt
?    6.506    776 pos.       97 -     318 PS50240|TRYPSIN_DOM Serine proteases, trypsin domain profile.
• 0 views • link
updated by Ram Ram • written by beatrice.cuche • beatrice.cuche

Please, see: Problems running ps_scan.pl

• 0 views • link
written by bzamith26 • bzamith26

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