hmm2fetch(1)

📦 version 2.3.2, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 hmm2fetch(1) — the HMMER manual, but make it cute 💖

okay bestie, welcome to hmm2fetch, a lil section of the HMMER Manual that's about to become your new fave. buckle up 🎀

✨ NAME ✨

hmm2fetch — retrieve an HMM from an HMM database 🧚

🌸 SYNOPSIS 🌸

hmm2fetch [options] database name

🦋 DESCRIPTION 🦋

okay so hmm2fetch is this tiny lil utility (small but mighty, the way that matters 💅) that goes and retrieves an HMM called name from a HMMER model database called database — in a new format — and then prints that model straight to standard output. slay.

like, for example, hmm2fetch Pfam rrm grabs the RRM (RNA recognition motif) model from Pfam, if the environment variable HMMERDB is set to the location of the Pfam database. iykyk 🌈

the retrieved HMM file gets written in HMMER 2 ASCII format. no cap.

⚠️ okay so important: the database must have an associated GSI index file. it's not optional, bestie, it's giving mandatory. if you need to index an HMM database, use the program hmm2index. 🫶

💅 OPTIONS 💅

  • -h — print brief help; includes the version number and a summary of all the options, including expert options. the "just tell me everything" button 🎀
  • -n — interpret name as an HMM number instead of a name. numbering starts at 0. so for example, to fetch the first HMM from an HMM database called foo, you would do hmm2fetch -n 0 foo. zero-indexed, iconic behavior, periodt ✨

🔥 SEE ALSO 🔥

  • Master man page, with full list of and guide to the individual man pages: see hmmer2(1).
  • For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, http://hmmer.janelia.org/. 📚

Copyright (C) 1992-2003 HHMI/Washington University School of Medicine. Freely distributed under the GNU General Public License (GPL). See the file COPYING in your distribution for details on redistribution conditions. 📜

💜 AUTHOR 💜

Sean Eddy HHMI/Dept. of Genetics Washington Univ. School of Medicine 4566 Scott Ave. St Louis, MO 63110 USA http://www.genetics.wustl.edu/eddy/

and that's the whole page, bestie 💖 this one's from HMMER 2.3.2, dated Oct 2003, and it lives on the hmm2fetch(1) page. mwah, go fetch some models 🦋✨🎀

📦 where this page comes from