GTOP(1)

✨ GTOP(1) ✨

okay bestie, this is a page from the pftools manual set — it's gtop, and it's giving ✨profile format glow-up✨ energy 💅

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🌸 NAME 🌸

gtop — convert a profile in GCG format into PROSITE format 🦋

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🎀 SYNOPSIS 🎀

gtop      [ -ahls ] [ -E gap_extend ] [ -F rescale ] [ -G gap_open ] [
          -O offset ] gcg_profile | - [ parameters ]

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💖 DESCRIPTION 💖

so basically, gtop takes a profile that was made by the GCG program ProfileMake (or by any GCG-compatible profile-building program) and turns it into PROSITE format. It can optionally rescale the profile while it's at it. The result goes straight to standard output, no cap. 🫶

On the way in, gtop divides every single weight in the profile by 100 — that's just what GCG programs do, it's their whole thing.

On the way out, profile scores get multiplied by the rescaling factor F and then rounded to the nearest integer. 🔢

Now the gap weighting, and this is the part where people get confused so listen up:

• If symmetric gap weighting mode is chosen, the gap opening weights are divided by 2 and assigned to the MI, MD, IM, and DM transition scores.
• If asymmetric gap weighting mode is chosen, the gap opening weights are left unchanged and assigned to the MI and MD transition scores only.

If you give it no argument at all, the program just tries to read the GCG formatted profile from the standard input. easy ✨

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💅 OPTIONS 💅

• gcg_profile — the input GCG profile. If you swap the filename out for a -, gtop will read the input profile from stdin instead. 🍓
• -a — apply asymmetric gap weighting mode (peep the DESCRIPTION section, bestie, it's all up there).
• -h — display the usage help text. bless 🙏
• -l — remove the output line length limit. Individual lines of the output profile are allowed to exceed a length of 132 characters, which means you don't have to wrap them over several lines anymore. iconic.
• -s — apply symmetric gap weighting mode (this is the default, fyi) (see the DESCRIPTION section).
• -E gap_extend — gap extension penalty. Default: 0.05
• -F rescale — score rescaling factor. Default: 100
• -G gap_open — gap opening penalty. Default: 4.5
• -O offset — output score offset. This value gets added to all profile match scores, and it happens after the multiplication by the rescaling factor F. Default: 0

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⭐ PARAMETERS ⭐

Note: for backwards compatibility, release 2.3 of the pftools package will still parse the version 2.2 style parameters — but bestie, these are deprecated 😭 and you should be using the corresponding option instead (refer to the OPTIONS section, it's right up there).

• E=# — gap extension penalty. Use option -E instead.
• F=# — output score rescaling factor. Use option -F instead.
• G=# — gap opening penalty. Use option -G instead.
• O=# — output score offset. Use option -O instead.

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🌈 EXAMPLES 🌈

(1)

gtop -G 1.0 -E 1.0 -F 50 sh3.gpr | pfsearch -far - sh3.seq | sort -nr

First it converts the GCG profile 'sh3.gpr' into PROSITE format. Then it searches the protein library 'sh3.seq' with that reformatted profile, which generates a sorted list of optimal alignment scores. 🔥

The pfsearch(1) option -r makes alignment scores come out expressed in raw score units, iykyk. And 'sh3.seq' contains 20 SH3 domain-containing protein sequences from SWISS-PROT release 32. no big deal 💜

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👑 EXIT CODE 👑

When gtop finishes its task successfully, it returns an exit code of 0. 🎉

If an error happens, 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 still be completed anyway? Warnings get issued on standard error. not me being dramatic about it 💀

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💀 BUGS 💀

gtop defines SCORE=0; N_SCORE=0; for the mandatory cut-off level zero. These parameters should be changed to more reasonable values using a text editor, prior to profile search operations. so yeah, go fix those by hand, bestie, it's a whole thing 🙈

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🦋 SEE ALSO 🦋

pfsearch(1), pfscan(1), pfmake(1), sort(1)

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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, bestie 💖 this was pftools version 2.3, dated April 2003 — shoutout to the pftools girlies, periodt ✨🎀