PFSCAN(1)

🦋 PFSCAN(1) — the pftools girlies' guide 🦋

okay so bestie, welcome to pfscan, a certified icon from the pftools package 💅 it scans your sequence against a whole library of profiles and it does NOT miss. buckle up, we're going through every single flag because I refuse to let you fumble this.

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✨ NAME ✨

pfscan — scan a protein or DNA sequence with a profile library 🧬

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🌸 SYNOPSIS 🌸

pfscan    [ -abdfhlLmruksvxyz ] [ -C cut_off ] [ -M mode_nb ] [ -W width
          ] [ sequence | - ] [ profile_library | - ] [ parameters ]

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💜 DESCRIPTION 💜

So what this does, fr fr: pfscan compares a protein or nucleic acid sequence against a profile library. The result? An unsorted list of profile-sequence matches, written straight to standard output. no sorting, no glow-up, just the matches, raw. 🙈

A bunch of different output formats with different info can be picked via the options -l, -L, -r, -k, -s, -x, -y and -z (yes that's a lot of letters, we'll get to each one, breathe).

The file sequence holds a sequence in EMBL/SWISS-PROT format — that's what it assumes by default — or in Pearson/Fasta format, and you tell it that with option -f. The profile_library file holds a library of profiles in PROSITE format. And if you drop a - instead of one of the filenames, that data gets read from standard input instead. cute, flexible, we love her. 💖

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👑 OPTIONS 👑

• sequence — your input query sequence. This DNA or protein sequence is what gets searched against the library of PROSITE profiles. The content of the file has to be either EMBL/SWISS-PROT (the default) or Pearson/Fasta format (that's option -f, babes). If you swap the filename for a -, pfscan reads the input sequence from stdin. 🌈
• profile_library — the library of PROSITE profiles. This file should have one or several PROSITE profiles in it, and your query sequence gets matched against them. Each entry in the library needs to be separated from the next by a line containing only the // code. And yeah, if you swap the filename for a -, pfscan reads the profile library from stdin. 🫶
• -a — report optimal alignment scores for all profiles, regardless of the cut-off value. heads up: this option simultaneously forces DISJOINT=UNIQUE. ⭐
• -b — search the complementary strand of the DNA sequence too. both strands, because why not. 🧬
• -f — input sequence is in Pearson/Fasta format. 📄
• -h — display usage help text. the classic cry-for-help flag, we've all been there. 😭
• -l — indicate the value of the highest cut-off level exceeded by the match score, in the output list. 🔢
• -L — indicate by character string the highest cut-off level exceeded by the match score, in the output list. (not the number, the vibe) ✨

Note: the generalized profile format includes a text string field to specify a name for a cut-off level. The -L option causes the program to display the first two characters of this text string (usually something like '!', '?', '??', etc.) at the beginning of each match description. 👀

• -m — report individual matches for circular profiles. If the profile is circular, each match between a sequence and a profile can be composed of a stretch of individual matches of the profile. By default, pfscan reports only the total matched region. When this option is set, detailed information for each individual match gets output as well. 🌀

Note: the scoring system for most circular profiles has been optimized to find total matches, therefore the normalized scores of individual matches of a circular profile to a sequence should be considered with caution. ⚠️

• -r — use raw scores rather than normalized scores for match selection. The normalized score is not printed. 🙅♀️
• -u — forces DISJOINT=UNIQUE. periodt. 💅
• -C cut_off — cut-off level to be used for match selection. The value of cut_off should be the numerical identifier of a cut-off level defined in the profile. The raw or normalized score of this level then gets used to include profile-to-sequence matches in the output list. If the specified level does not exist in the profile, the next higher level defined is used instead (when cut_off is negative) or the next lower level defined is used instead (when cut_off is positive). 🎚️
  • Type: integer
  • Default: 0
• -M mode_nb — normalization mode to use for score computation. mode_nb specifies which normalization mode defined in the profile should be used to compute the normalized scores for profile-to-sequence matches. This option will override the profile's PRIORITY parameter. If the specified normalization mode does not exist in the profile, an error message gets output to standard error and the search is interrupted. 💀
  • Type: integer
  • Default: lowest priority mode defined in the profile

🎀 Output modifiers 🎀

• -d — limit profile description length. If this option is set, the description of the profile on the header line gets limited in length. If the match information is longer than the output width specified using option -W, the profile description will not be printed. Else the description gets truncated to fit the -W value. By default, the profile description is not truncated. This option can not be used when option -k is set. ✂️
• -k — use xpsa(5) headers for output. When this option is set, all output types (see below) will use an xpsa(5) style header line. This format uses keyword=value pairs to output alignment parameters. It is useful to transfer information between different sequence alignment tools. 🤝
• -s — list the sequences of the matched regions as well. The output will be a Pearson/Fasta-formatted sequence library. 📚
• -v — suppress sequence/profile parsing warnings. If this option is set, no warning messages get printed on stderr. Only fatal errors will be reported. 🚨

this option should be used with caution. fr, be careful with her.

• -x — list profile-sequence alignments in psa(5) format. Please refer to the corresponding man page for more information. 📖
• -y — display alignments between the profile and the matched sequence regions in a human-friendly pairwise alignment format. 🥰 (yes, human-friendly, unlike some of her sisters)
• -z — indicate starting and ending position of the matched profile range. The latter position will be given as a negative offset from the end of the profile. Thus the range [ 1, -1] means entire profile. 📍
• -W width — set alignment output width. The value of width specifies how many residues will be output on one line when any of the -s, -x or -y options is set. 📏
  • Type: integer
  • Default: 60

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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. like, use the option, bestie. 🙏

• L=# — cut-off level. Use option -C instead, not -L. ⚠️
• W=# — output width. Use option -W instead. ⚠️

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🌟 EXAMPLES 🌟

1. ✨

pfscan -s GTPA_HUMAN prosite13.prf

Scans the human GAP protein for matches to profiles in PROSITE release 13. The file GTPA_HUMAN contains the SWISS-PROT entry P20936|GTPA_HUMAN. The profile library file prosite13.prf contains all profile entries of PROSITE release 13. The output is a Pearson/Fasta-formatted sequence library containing all sequence regions of the input sequence matching a profile in the profile library. 🧬

2. ✨

pfscan -by -C 2 CVPBR322 ecp.prf

Scans both strands of plasmid PBR322 for high-scoring (level 2) E. coli promoter matches. The sequence file CVPBR322 contains EMBL entry J01749|CVPBR322. The profile library file ecp.prf contains a profile for E. coli promoters. The output includes profile-sequence alignments in a human-friendly format. 🦠

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🔥 EXIT CODE 🔥

On successful completion of its task, pfscan will return an exit code of 0. If an error occurs, a diagnostic message gets 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. 👀

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💀 BUGS 💀

If the match selection is based on normalized scores (i.e. option -r is not set), rounding errors can lead to the exclusion of some matches even if the raw score is above or equal to the specified cut-off level score. she's doing her best but math is math, bestie. 😭

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🫶 SEE ALSO 🫶

pfsearch(1), pfmake(1), psa(5), xpsa(5)

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💜 AUTHOR 💜

The pftools package was developed by Philipp Bucher. Any comments or suggestions should be addressed to <pftools@sib.swiss>. 📬

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and that's the whole page, you ate it up. this was pftools 2.3, dated July 2003, and yes she's still that girl 💅✨ go scan something cute, ily, byeee 🎀🦋