PTOH(1)

💖 PTOH(1) — the pftools girlies' guide 💖

okay bestie, so this page lives in the pftools</pftools> manual set, and it's all about a little program called ptoh. it's giving "glow-up for profiles" and honestly? iconic. let's get into it 🦋

✨ NAME ✨

ptoh — converts a PROSITE formatted profile into an approximately equivalent HMM 🌸

✨ SYNOPSIS ✨

ptoh      [ -fFhs ] [ -D del_to_del ] [ -I ins_to_ins ] [ -L log_base ]
          [ profile | - ] [ random_model ] [ parameters ]

✨ DESCRIPTION ✨

so basically, ptoh takes a PROSITE formatted generalized profile and turns it into an approximately equivalent hidden Markov model — HMMER1 format by default, or SAM format if you ask nicely. the file profile is a nucleic acid or protein profile in PROSITE format, no cap. and if you write - instead of a filename? it reads the profile straight from standard input, periodt. 💅

the random_model file holds a simple null-model in the format used by the HMM search programs of the HMMER1 package. the result gets written to standard output. slay.

the profile-to-HMM conversion method is described in Bucher et al. (1996). every profile score that corresponds to transitions not supported by the HMM architectures of the SAM and HMMER1 packages gets ignored — sorry babes, they just don't make the cut 🙈. if no random model is given on the command line, the null model from the GENERAL_SPEC data block of the profile is used instead. and if that's also missing? a flat residue distribution is assumed. the show must go on ✨

✨ OPTIONS ✨

• profile — the input PROSITE generalized profile. the motif described by the profile gets converted into an approximately equivalent HMM. if you swap the filename out for a -, ptoh will read the input profile from stdin. very demure, very mindful 🎀
• random_model — the input random model file. this file should contain a simple null-model using the same residue alphabet as the profile. gotta match, bestie 🧚
• -f — generates free insert-modules (FIMs) at the beginning and at the end of the model, which approximately emulate domain-global or semi-global alignment mode (see Bucher et al. 1996). 🔥
• -F — generates free insert-modules (FIMs) at the beginning and at the end of the model, which approximately emulate local alignment mode. yes queen, fragment-search energy 👑
• -h — displays the usage help text.

note: the meaning of this option has changed between version 2.2 and the current release of the pftools package. no option is needed to get HMMER1 output format, because it's the default (see option -s). so like… don't come at -h for HMMER1, it's not that girl anymore 💀

• -s — output in SAM format.
• -D del_to_del — delete-to-delete transition probabilities. these are used in conjunction with FIMs (options -f, -F). this value gets imposed on all delete-to-delete transitions of the model. the other outgoing transitions from the affected delete states will be renormalized to satisfy the "sum to one" requirement. note that the application of the D parameter precedes the application of the I parameter. delete-to-delete probabilities at the beginning and at the end of the model may therefore change again as a result of renormalizations following the application of the I parameter. it's a whole pipeline, ok? Default: 0.9
• -I ins_to_ins — insert-to-insert transition probabilities. these are used in the FIMs (options -f, -F). this value gets imposed on the first and the last match-to-insert and insert-to-insert transition probabilities of the model. the other outgoing transitions of the affected states get renormalized such as to satisfy the "summing to one" requirement. and if the -F option is simultaneously set, the I parameter will also be imposed on the insert-to-delete transition probability at the beginning, and on the delete-to-insert transition probability at the end of the model. multitasking icon 💅 Default: 0.99
• -L log_base — logarithmic base. specifies the logarithmic base used for conversion of the profile scores into HMM probabilities (the profile scores are interpreted as log-odds ratios, see Bucher et al. 1996). this value overwrites the logarithmic base specified within the profile by the optional LOG_BASE parameter. rude but valid ✨ Default: 1.0233739 (1/30 bit units)

✨ 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, bestie) should be used instead.

• D=# — delete-to-delete transition probabilities. use option -D instead. 🫶
• I=# — insert-to-insert transition probabilities. use option -I instead. 🫶
• L=# — logarithmic base. use option -L instead. 🫶

✨ EXAMPLES ✨

1. ``` ptoh -Fs -L 1.0233739 sh3.prf standard.random > sh3.hmm

generates a SAM formatted HMM for the SH3 domain from a profile. the file `sh3.prf` contains the source profile in PROSITE format. the file `standard.random` contains the null-model used for conversion of the log-odds ratios into probabilities. the logarithmic base `1.0233739` corresponds to 1/30 bits, the implicit scale of the profile. and the `-F` option causes the HMM to emulate local alignment (fragment search) mode. honestly? a whole serve 🔥

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# ✨ EXIT CODE ✨

on successful completion of its task, `ptoh` 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 get issued on standard error. it's not mad, just disappointed 😭

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# ✨ REFERENCES ✨

Bucher P, Karplus K, Moeri N & Hofmann, K. (1996). A flexible motif search technique based on generalized profiles. *Comput. Chem.* 20:3-24.

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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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<purple>pftools 2.3</purple> · <lavender>April 2003</lavender> — that's the version and the date, babes. go forth and convert some profiles, bestie, you're gonna eat 💖✨🎀🦋🌸💅🫶