hmmalign(1)

✨ hmmalign — the manual, but make it a group chat ✨

okay so this is hmmalign(1), straight out of the HMMER Manual bestie 💖 and no cap, it's the glow-up tool for getting your lil sequences lined up against a profile. Let's get into it 🦋

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🌸 NAME 🌸

hmmalign — align sequences to a profile 💅

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🎀 SYNOPSIS 🎀

hmmalign [options] hmmfile seqfile

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✨ DESCRIPTION ✨

So what we're doing here is a multiple sequence alignment of literally every sequence in seqfile, and the way we do it is by aligning them individually to the profile HMM sitting in hmmfile. The brand-new alignment goes straight to stdout. iconic behaviour tbh 🌈

Now, hmmfile should contain only a single profile. If it's got more than one in there? girlypop, only the first profile in the file gets used. the rest are just standing there 💀

And here's a fun one: either hmmfile or seqfile (but not both, okay?? not both 😭) can be - (a dash), which means read that input from stdin instead of from a file. choose one. one of them. please 🙈

The sequences in seqfile get aligned in unihit local alignment mode. Which means — and this is important — they should already be known to contain only a single domain (or a fragment of one). If the optimal alignment decides some residues are nonhomologous (that's the N and C states, iykyk), those residues are still included in the resulting alignment, they just get shoved out to the outer edges. lowkey rude but that's the vibe.

want those unaligned nonhomologous residues trimmed off the result? that's the --trim option, bestie ✂️✨

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💅 OPTIONS 💅

• -h — Help! Prints a brief lil reminder of the command line usage plus all the available options. your girl's got your back 🫶
• -o <f> — Send the output alignment to file <f> instead of to stdout. cute little redirect, no drama.
• --mapali <f> — Merge the existing alignment in file <f> into the result — and heads up, <f> has to be exactly the same alignment that was used to build the model in hmmfile. How does it do that? Using a map of alignment columns to consensus profile positions that's stored inside hmmfile. ✨ The multiple alignment in <f> will be exactly reproduced in its consensus columns (as defined by the profile), but the displayed alignment in insert columns may be altered — because insertions relative to a profile are, by convention, considered unaligned data. just how the culture works 💁‍♀️
• --trim — Trims the nonhomologous residues (the ones assigned to N and C states in the optimal alignments) out of the resulting multiple alignment output. the glow-up filter 🎀
• --amino — Asserts that the sequences in seqfile are protein, bypassing alphabet autodetection. say it with your chest 🧬
• --dna — Asserts that the sequences in seqfile are DNA, bypassing alphabet autodetection.
• --rna — Asserts that the sequences in seqfile are RNA, bypassing alphabet autodetection.
• --informat <s> — Asserts that the input seqfile is in format <s>, bypassing format autodetection. Common choices for <s> include: fasta, embl, genbank. Alignment formats also work; common choices include: stockholm, a2m, afa, psiblast, clustal, phylip. For more info — and for codes for some less common formats — see main documentation. And yes, the string <s> is case-insensitive (fasta or FASTA both work, we don't gatekeep case 💜).
• --outformat <s> — Writes the output alignment in format <s>. Common choices for <s> include: stockholm, a2m, afa, psiblast, clustal, phylip. The string <s> is case-insensitive (a2m or A2M both work). Default is stockholm. periodt 💅

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🦋 SEE ALSO 🦋

• Peep hmmer(1) for a master man page with a whole list of all the individual man pages for programs in the HMMER package. it's the mothership 👑
• For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (http://hmmer.org/). go read, bestie 📖

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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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and that's the whole page, bestie 🫶 HMMER 3.4, dated Aug 2023 — written up all cute for ya, hmmalign(1) and all 💖 mwah, go align something gorgeous ✨