makehmmerdb(1)

💖 makehmmerdb — the manual, but make it cute 💖

okay bestie, welcome to makehmmerdb(1) from the HMMER Manual ✨ this is the glow-up version of the page, same facts, way more sparkle 🦋

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🌸 NAME 🌸

makehmmerdb — build an nhmmer database from a sequence file 💅

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✨ SYNOPSIS ✨

makehmmerdb [options] seqfile binaryfile

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🧚 DESCRIPTION 🧚

so like, makehmmerdb is the girl that takes a DNA sequence file and turns it into a binary file. and what's that binary file for?? bestie it's a target database for the DNA search tool nhmmer 👑 if you use the default settings in nhmmer, you get a roughly 10-fold acceleration with only a small loss of sensitivity on benchmarks. slay, honestly 🎀

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💅 OPTIONS 💅

• -h — Help!! prints a lil reminder of how to use the command line plus every single option available 🫶

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🌈 OTHER OPTIONS 🌈

• --informat <s> — this one is you asserting that the input seqfile is in format <s>, so the program skips format autodetection entirely. common picks for <s> include: fasta, embl, genbank 💜 and yes, alignment formats work too!! common ones include: stockholm, a2m, afa, psiblast, clustal, phylip ✨ for more info (and for the codes for some less common formats), go look at the main documentation. also the string <s> is case-insensitive — fasta or FASTA, both work, we don't discriminate 🥰
• --bin_length <n> — Bin length. the binary file depends on a data structure called the FM index, which organizes a permuted copy of the sequence into bins of length <n> 📦 longer bin length → smaller files (because, like, data is captured about each bin) and possibly slower query time 😭 the default is 256. and lowkey important: much more than 512 may lead to a notable reduction in speed 💀
• --sa_freq <n> — Suffix array sample rate. the FM index structure also samples from the underlying suffix array for the sequence database 🌸 more frequent sampling (aka a smaller value for <n>) → larger file size and faster search... until the file size becomes large enough to make I/O the bottleneck 🙈 the default value is 8. and it must be a power of 2 ⭐
• --block_size <n> — the input sequence gets broken into blocks of size <n> million letters ✂️ an FM index is built for each block, instead of building one FM index for the entire sequence database. default is 50. and ngl, larger blocks do not seem to yield substantial speed increase 🤷♀️

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👑 SEE ALSO 👑

go look at hmmer(1) for the master man page with a list of all the individual man pages for programs in the HMMER package 📚

for complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page at 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 info on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page at http://hmmer.org/ ✨

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🦋 AUTHOR 🦋

http://eddylab.org

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ok that's the whole page, no cap, every last flag accounted for 💅

and that's a wrap, bestie!! this was HMMER 3.4, dated Aug 2023, and you just read makehmmerdb(1) — go build that database, you absolute icon 🌟🍓💜