PFSCALE(1)

✨ PFSCALE(1) ✨

okay bestie, gather round, because we're talking about pfscale from the pftools manual, and she is that girl 💅. Short version: she fits the parameters of an extreme-value distribution to a profile score list. Longer version below, and yes, every single flag is coming with us 🫶

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🌸 NAME 🌸

pfscale — fit parameters of an extreme-value distribution to a profile score list 💖

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🎀 SYNOPSIS 🎀

pfscale   [ -hl ] [ -L log_base ] [ -M mode_nb ] [ -N db_size ] [ -P
          upper_limit ] [ -Q lower_limit ] [ score_list | - ] [ profile
          ] [ parameters ]

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💜 DESCRIPTION 💜

So here's the vibe: pfscale fits the two parameters of an extreme-value distribution to a sorted score distribution that you got by searching a sequence database with a profile. The file score_list is a sorted list of profile match scores generated by pfsearch. And if you pass - instead of a filename, bestie, the score list gets read from standard input. The result? Written to standard output. Periodt. ✨

If you hand over the original profile as the second argument, then the normalization function with the lowest mode number or the lowest priority number specified within the profile gets updated, such as to produce -Log10 per-residue E-values. But if that second argument is omitted, the output is a header line containing the normalization parameters followed by a modified score list, showing score rank, original raw scores, log-cumulative frequencies and corresponding normalized scores next to each other. Iconic layout, no notes. 😌

💀 Heads up: this program implements the significance estimation procedure for profile match scores described in Hofmann & Bucher (1995). It has been used for the calculation of the normalization parameters of all profiles in the PROSITE database. Like, all of them. Main character energy fr fr.

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✨ OPTIONS ✨

• score_list — Input score list. The file has to contain a sorted list of scores. The first field of each line is treated as being a score, and all the other fields on that same line are just ignored, we don't see them, they're not in our lane 🙈. The different fields of each line should be delimited by whitespaces. And if the filename gets replaced by a -, pfscale will read the score list from stdin.
• profile — Optional profile file. If you specify a filename, the profile will be parsed and either the lowest priority mode or the mode number specified with option -M will be scaled. All cut-off levels which use the specified mode number will also be updated. she's thorough like that 💅
• -h — Display usage help text. simple. clean. iconic.
• -l — Remove output line length limit. Individual lines of the output profile can exceed a length of 132 characters, removing the need to wrap them over several lines. Let her stretch out, she's been in a box all day 😭
• -L log_base — Logarithmic base of the parameters of the estimated extreme-value distribution. The parameters reported by pfscale are expressed as logarithms and thus can be inserted directly into a linear normalization function defined in a generalized profile.
  • Default: 10
• -M mode_nb — Mode number to scale. This defines which mode number (and implicitly which cut-off level) of the input PROSITE profile should be scaled. It overrides the default behaviour of scaling only the normalization mode with the lowest priority (or lowest mode number). All cut-off levels defined in the profile as using this mode number (via the MODE keyword) will be updated as well. so if you want a specific mode to be the chosen one, this is your moment ⭐
• -N db_size — Size of the database from which the input score list was derived. The searched database is typically a shuffled version of a real protein or nucleotide sequence database.
  • Default: 14147368 (size of SWISS-PROT release 30 and shuffled derivatives of it).
• -P upper_limit — Upper threshold of the probability range to which the extreme-value distribution will be fitted. For instance: if N=10'000'000 and P=0.0001 then profile match scores below rank 1000 in the sorted input list (corresponding to occurrence probabilities > 0.0001) will be ignored.
  • Default: 0.0001
• -Q lower_limit — Lower threshold of the probability range to which the extreme-value distribution will be fitted. For instance: if N=10'000'000 and Q=0.000001 then profile match scores above rank 10 in the sorted input list (corresponding to occurrence probabilities < 0.000001) will be ignored.
  • Default: 0.000001

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🦋 PARAMETERS 🦋

⚠️ Note: for backwards compatibility, release 2.3 of the pftools package will parse the version 2.2 style parameters, but these are deprecated and the corresponding option (refer to the options section) should be used instead. bestie please stop using these, I'm begging 🙏

• L=# — Logarithmic base. Use option -L instead.
• M=# — Mode number. Use option -M instead.
• N=# — Database size. Use option -N instead.
• P=# — Upper probability threshold. Use option -P instead.
• Q=# — Lower probability threshold. Use option -Q instead.

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💖 EXAMPLES 💖

1. Let's cook 🍓:

pfsearch -fr -C 200 sh3.prf shuffle20.seq | sort -nr | pfscale -P
0.0001 -Q 0.000001 -

this derives score-normalization parameters for the SH3 domain profile in file sh3.prf. The file shuffle20.seq contains a window-shuffled derivative of SWISS-PROT release 30 in Pearson/Fasta format (window-size 20). Note that the implicit default of N corresponds to the size of this database and thus needs not to be specified on the command line. The cut-off value 200 for the pfsearch(1) option -C will produce about 2000 matches completely covering the range defined by the command line parameters -P and -Q of pfscale. A suitable cut-off value has to be guessed in advance by computing a few optimal alignment scores for random sequences. yes you have to guess, no I don't make the rules 😭

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🌈 EXIT CODE 🌈

On successful completion of its task, pfscale will return an exit code of 0 🎉. If an error occurs, a diagnostic message will be output on standard error and the exit code will be different from 0 💀. And when conflicting options were passed to the program but the task could nevertheless be completed, warnings will be issued on standard error. she'll do it, but she will be talking about it 🙈

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🧚 NOTES 🧚

1. The current version of pfscale does not yet support the xpsa(5) output format produced by pfscan(1) or pfsearch(1). The score list should therefore be generated without the pfscan(1) and pfsearch(1) option -k. so basically: no -k. none. not today 🚫

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👑 REFERENCES 👑

Hofmann K & Bucher P. (1995). The FHA-domain: a nuclear signalling domain found in protein kinases and transcription factors. Trends Biochem. Sci. 20:47-349.

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⭐ SEE ALSO ⭐

pfsearch(1), pfscan(1), xpsa(5)

iykyk 💜

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💌 AUTHOR 💌

The pftools package was developed by Philipp Bucher. Any comments or suggestions should be addressed to <pftools@sib.swiss>. slide into the inbox, she reads everything 🫶

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okay that's the whole page bestie, you ate that. this was the pftools 2.3 manual, dated August 2003, and if you ever need her again just run man pfscale. 💅✨🌸