HMMER(1)

HMMER 💖

okay bestie, welcome to the HMMER Manual — this is the big group-chat summary page for the whole HMMER(1) package, and honestly? it's iconic. profile HMMs for biological sequence analysis, no cap. 🧬✨

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🌸 NAME 🌸

HMMER — profile HMMs for biological sequence analysis 💅

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✨ SYNOPSIS ✨

here's the whole squad, one line each. every single one of them has their own man page too, so this is basically the intro slide 🫶

• hmmalign — align sequences to a profile
• hmmbuild — construct profiles from multiple sequence alignments
• hmmconvert — convert profile file to various formats
• hmmemit — sample sequences from a profile
• hmmfetch — retrieve profiles from a file
• hmmlogo — produce a conservation logo graphic from a profile
• hmmpgmd — daemon for database search web services
• hmmpress — prepare a profile database for hmmscan
• hmmscan — search sequence(s) against a profile database
• hmmsearch — search profile(s) against a sequence database
• hmmsim — collect profile score distributions on random sequences
• hmmstat — summary statistics for a profile file
• jackhmmer — iteratively search sequence(s) against a sequence database
• makehmmerdb — build nhmmer database from a sequence file
• nhmmer — search DNA/RNA queries against a DNA/RNA sequence database
• nhmmscan — search DNA/RNA sequence(s) against a DNA/RNA profile database
• phmmer — search protein sequence(s) against a protein sequence database
• alimask — calculate and add column mask to a multiple sequence alignment

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👑 DESCRIPTION 👑

HMMER is a whole suite of programs for biological sequence alignment and database homology search. the way it works is it uses probabilistic models called "profile hidden Markov models" (profile HMMs) to represent the likely evolutionary homologs of a single sequence, or of a multiple alignment of a sequence family. and like, a main avenue of research here is making the evolutionary predictive models in HMMER better, so they can recognize and accurately align homologs that are increasingly remote — distant in time. ⏳

HMMER is also used as an organizational tool, fr — it groups the exponentially growing number of biological sequences into a vastly smaller set of well-annotated sequence families. new sequences can be annotated by comparison against curated sequence family databases of prebuilt HMMER profiles, in addition or instead of comparison to the entire sequence database. databases such as Pfam, SMART, and TIGRfams, among others, are based on this principle. 🫶

HMMER is used in three main modes:

1. to search a sequence database for new homologs of a sequence or a sequence family
2. to search a profile database (like Pfam) to find what known family a query sequence belongs to, or what domains it has
3. to automatically construct large multiple alignments (i.e. with an effectively unlimited number of sequences) using a profile representative of a sequence family

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🦋 so, scenario one: you've got an alignment 🦋

suppose you have a multiple sequence alignment of a sequence family of interest, and you want to search a sequence database for additional homologs. the hmmbuild program builds profile(s) from multiple alignment(s). the hmmsearch program searches protein profile(s) against a protein sequence database, and nhmmer searches nucleotide profile(s) against a nucleotide sequence database. 💖

🌈 scenario two: you've got ONE sequence 🌈

suppose you have a single sequence of interest, and you want to search a sequence database for additional homologs. the phmmer program searches a single protein sequence against a protein sequence database. the jackhmmer program does the same thing but iteratively — homologs detected in a previous round are incorporated into a new profile, and the new profile is searched again. phmmer is used like BLASTP, and jackhmmer is used like a protein PSI-BLAST. the nhmmer program searches a single nucleotide sequence against a nucleotide sequence. 🔥

💜 scenario three: you're using a profile HMM database 💜

suppose you have sequence(s) that you want to analyze using a HMMER-based profile HMM database like Pfam (http://pfam.sanger.ac.uk). the hmmpress program formats a profile HMM flatfile (such as the file you would download from Pfam) into a HMMER binary database. the hmmscan program searches protein sequence(s) against that database. the nhmmscan program can similarly search nucleotide sequence(s) against a pressed database of nucleotide profiles, such as from Dfam (http://dfam.janelia.org). 🌸

🎀 scenario four: you want to align SO many sequences 🎀

suppose you want to align lots of sequences. you can construct a manageably small alignment of a representative set of sequences, build a profile with hmmbuild, and use the hmmalign program to align any number of sequences to that profile. main character move tbh. 💅

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🧚 the auxiliary tools 🧚

HMMER also includes some auxiliary tools for working with large profile databases. hmmfetch fetches one or more profiles from a database. hmmstat prints summary statistics about a profile file.

for compatibility with other profile software and previous versions of HMMER, the hmmconvert program converts profiles to a few other formats. and like — they intend to add more support for other formats over time. 👀

the hmmemit program generates (simulates) "homologous" sequences by sampling from a profile. it can also generate a "consensus" sequence. ⭐

the hmmsim program is a simulator used for collecting statistics about score distributions on random sequences.

each program has its own man page. iykyk. 🍓

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🔍 SEE ALSO 🔍

this is a summary man page for the entire HMMER3 package. see individual man pages [hmmbuild(1), for example] for usage, options, and description of each program in the package.

for complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (http://hmmer.org/). 💖

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💀 COPYRIGHT 💀

Copyright (C) 2023 Howard Hughes Medical Institute. Freely distributed under the BSD open source license.

for additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (http://hmmer.org/). 🫶

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🌟 AUTHOR 🌟

http://eddylab.org

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okay that's the whole page bestie, you ate that. go build a profile. periodt. 💅✨

HMMER 3.4 — Aug 2023 — HMMER(1) 🎀 that's the version and the date, mwah, bye!! 👑🦋💜