HTOP(1)

🌸 HTOP(1) — the htop page, bestie edition 🌸

okay so you opened the htop manual from the pftools set and you're like "what is this" — don't worry, I got you. Let me put you on. 🫶

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✨ NAME ✨

htop — takes a HMMER ASCII-formatted HMM and turns it into an equivalent PROSITE profile. that's the whole job. she's a converter, she's iconic, she does one thing and she does it. 💅

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✨ SYNOPSIS ✨

htop [ -fhilos ] [ -B norm_logbase ] [ -C cut_off ] [ -F multiplier
] [ -H init/term_score ] [ -L score_logbase ] [ -M
nb_unprotect ] [ -P percent_unprotect ] [ -Q odds_ratio ]
hmm_file | - [ random_model ] [ parameters ]

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✨ DESCRIPTION ✨

so htop converts a hidden Markov model (HMM) into an equivalent PROSITE formatted generalized profile. glow-up of the century honestly.

the input hmm_file is a nucleic acid or protein HMM in HMMER ASCII-format. and then there's the random_model file, which holds a simple null-model in the format that the HMM search programs of the HMMER1 package use.

🚨 important bestie: that random model is only effective in conjunction with the -o option (old HMMER1 format). like, only then. otherwise it's just sitting there.

and if you omit it entirely? then a random model gets used that consists of the average residue probabilities of the insert states. she improvises. 💁

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✨ OPTIONS ✨

• hmm_file — the input HMM ASCII-file. by default htop is expecting a HMMER2 formatted HMM. but if you set the -o option, the file should be in HMMER1 ASCII format instead. and if you replace the filename with a -, htop will read the input HMM from stdin. yes, she takes it from the pipe, we love a flexible queen.
• random_model — the input random model file. only used in conjunction with HMMER1 HMMs (see option -o). this file should contain a simple null-model using the same residue alphabet as the hmm_file. matching alphabets, as they should. 💅
• -f — emulate HMM fragment search (only effective with old HMMER1 format). when you give this as input to the pftools programs pfsearch(1) or pfscan(1), the resulting profile will behave like the original HMM searched with the HMMER1 program hmmfs. the default mode is to emulate HMM local search implemented in the HMMER1 program hmmls. so -f is the plot twist, the default is the normie route.
• -h — display usage help text. your girl is confused, your girl asks for help, no shame. 🎀
• -i — force all insert extension scores to be zero. just zero. all of them. cold. 💀
• -l — remove the output line length limit. individual lines of the output profile can then exceed a length of 132 characters, which removes the need to wrap them over several lines. long lines, unbothered, moisturized.
• -o — assume the input is in old HMMER1 ASCII format. since version 2.2, the pftools assume the HMMER2 format by default. so this is you saying "no actually, throwback".
• -s — implement semiglobal alignment mode. this option forces all external initiation scores to be identical to the internal initiation score at the beginning of the profile. likewise, the external termination scores are set to the value of the internal termination score at the end of the profile. symmetry!! we love to see it. ✨
• -B norm_logbase — logarithmic base to be used for normalization of profile match scores (only effective with old HMMER1 format). Default: 2.0
• -C cut_off — level zero cut-off value in normalized score units. Default: 8.5 (or 0.0 in conjunction with option -o)
• -F multiplier — output score multiplier. on output, all profile scores are multiplied by this factor and rounded to the nearest integers. only effective with HMMER2 format. Default: 100
• -H init/term_score — high-cost initiation/termination score (only effective in conjunction with the -s option). this score will be applied to all external and internal initiation and termination scores at path matrix positions where initiation or termination at low cost is not possible according to semiglobal alignment mode. Default: * (low-value)
• -L score_logbase — logarithmic base to be used for representation of profile scores (only effective in conjunction with old HMMER1 format). Default: 1.0233739 (1/30 bit units)
• -M nb_unprotect — maximal number of unprotected residues at the ends of the profile. Type: integer Default: 5 (meaning that the protected region starts at position 6)
• -P percent_unprotect — percent profile-length at the ends of the profile, which will not be included in the protected area. Type: real Default: 0 (range 0 to 100)
• -Q odds_ratio — position-independent odds ratio assumed for unknown residues. this parameter determines the default values for profile scores M0 and I0. note that the I0 scores may be over-written by the -i option. Default: 0.8

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✨ PARAMETERS ✨

📢 heads up: 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. so like… they still work, but they're giving expired. use the options. 🫠

• B=# — match score logarithmic base. Use option -B instead.
• C=# — level zero cut-off. Use option -C instead.
• F=# — output score multiplier. Use option -F instead.
• H=# — high-cost init/term score. Use option -H instead.
• L=# — profile scores logarithmic base. Use option -L instead.
• M=# — maximal number of unprotected residues. Use option -M instead.
• P=# — percentage of unprotected residues. Use option -P instead.
• Q=# — unknown residues odds ratio. Use option -Q instead.

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✨ EXAMPLES ✨

1. okay so bestie, watch this:

htop pfam_sh3.hmm > pfam_sh3.prf

that converts the HHMER2 formatted SH3 domain profile 'pfam_sh3.hmm' into a generalized PROSITE profile. ✨

and after this conversion, the following two commands:

hmmsearch --null2  pfam_sh3.hmm sh3.seq
pfsearch -fy -C 5.0 pfam_sh3.prf sh3.seq

should produce equivalent results in terms of raw scores and profile-sequence alignments (E-values and normalized scores will usually be different). and note that the program hmmsearch is from Sean Eddy's HMMER2 package (http://hmmer.wustl.edu/). 🔥

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✨ EXIT CODE ✨

on successful completion of its task, htop will return an exit code of 0. slay, no notes. 💖

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. so it's like… she did it, but she's side-eyeing you about it. 😭

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✨ SEE ALSO ✨

pfsearch(1), HMMER documentation

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✨ AUTHOR ✨

the pftools package was developed by Philipp Bucher. 👑

any comments or suggestions should be addressed to <pftools@sib.swiss>. she reads her inbox, fr fr.

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and that's the whole page, no cap. this was pftools 2.3, from May 2003 — yeah she's vintage, she's a classic, she's still serving. 🦋 mwah, go convert some profiles. 🎀✨