hmmer2(1)

🌸 hmmer2 — the HMMER manual, but make it a group chat 🌸

okay bestie, so this is the manual for HMMER (that's the profile hidden Markov model software), living in section 1 of the manual. buckle up, it's giving biology but make it statistical 💅

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✨ NAME ✨

HMMER — profile hidden Markov model software 🧬💖

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🌈 SYNOPSIS 🌈

so there's a whole squad of little programs and they all do their own thing. here's the roster, no cap:

hmm2align

• hmm2align — Align multiple sequences to a profile HMM. 🫶

hmm2build

• hmm2build — Build a profile HMM from a given multiple sequence alignment. 🏗️✨

hmm2calibrate

• hmm2calibrate — Determine appropriate statistical significance parameters for a profile HMM prior to doing database searches. 📊

hmm2convert

• hmm2convert — Convert HMMER profile HMMs to other formats, such as GCG profiles. 🔄

hmm2emit

• hmm2emit — Generate sequences probabilistically from a profile HMM. 🎲

hmm2fetch

• hmm2fetch — Retrieve an HMM from an HMM database. 📥

hmm2index

• hmm2index — Create a binary SSI index for an HMM database. 🗂️

hmm2pfam

• hmm2pfam — Search a profile HMM database with a sequence (i.e., annotate various kinds of domains in the query sequence). 🔍

hmm2search

• hmm2search — Search a sequence database with a profile HMM (i.e., find additional homologues of a modeled family). 👯

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🦋 DESCRIPTION 🦋

These programs use profile hidden Markov models (profile HMMs, iykyk) to model the primary structure consensus of a family of protein or nucleic acid sequences. literally that's the whole vibe. 🧬💜

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💅 OPTIONS 💅

okay so here's the tea. every single HMMER program, if you just run it with no arguments at all, will give you a brief lil summary of its command-line syntax and options. super chill. 🎀

But the moment you hit it with the single argument -h (that's help, bestie), the program gets verbose — it reports way more command-line usage info, including the rarely used, experimental, and expert options. 🙈 -h will also report version numbers, which are useful if you need to report a bug or a problem to me. 👑

Each HMMER program has its own man page that briefly summarizes command line usage. There's also a user's guide that came with the software distribution — it includes a tutorial introduction and more detailed descriptions of the programs. 📚✨

See http://hmmer.janelia.org/ for on-line documentation and the current HMMER release. 🌐

In general, no command line options should be needed by beginning users. The defaults are set up for optimum performance in most situations. periodt. 💅

here's how to read the option energy:

• Options that are single lowercase letters (e.g. -a) are "common" options that are expected to be frequently used and will be important in many applications. ⭐
• Options that are single uppercase letters (e.g. -B) are usually less common options, but also may be important in some applications. 🔥
• Options that are full words (e.g. --verbose) are either rarely used, experimental, or expert options. 👑

some experimental options are only there for my own ongoing experiments with HMMER, and may not be supported or documented adequately. so like… use those at your own risk bestie 😭

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🎀 SEQUENCE FILE FORMATS 🎀

In general, HMMER attempts to read most common biological sequence file formats. It autodetects the format of the file. It also autodetects whether the sequences are protein or nucleic acid. Standard IUPAC degeneracy codes are allowed in addition to the usual 4-letter or 20-letter codes. iconic behaviour honestly 🌈

Unaligned sequences

Unaligned sequence files may be in FASTA, Swissprot, EMBL, GenBank, PIR, Intelligenetics, Strider, or GCG format. These formats are documented in the User's Guide. 📖

Sequence alignments

Multiple sequence alignments may be in CLUSTALW, SELEX, or GCG MSF format. These formats are documented in the User's Guide. 📖

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🧚 ENVIRONMENT VARIABLES 🧚

For ease of using large stable sequence and HMM databases, HMMER looks for sequence files and HMM files in the current working directory as well as in system directories specified by environment variables. 🫶

• BLASTDB — Specifies the directory location of sequence databases. Example: /seqlibs/blast-db/. In installations that use BLAST software, this environment variable is likely to already be set. 💾
• HMMERDB — Specifies the directory location of HMM databases. Example: /seqlibs/pfam/. 🗄️

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and that's the whole page bestie, you ate it 💖 this was HMMER 2.3.2, from Oct 2003, documented in the HMMER Manual, section hmmer2(1) — go forth and profile-hide those Markov models, mwah 🎀✨👑