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makehmmerdb(1) HMMER Manual makehmmerdb(1)


makehmmerdb - build nhmmer database from a sequence file


makehmmerdb [options] seqfile binaryfile


makehmmerdb is used to create a binary file from a DNA sequence file. This binary file may be used as a target database for the DNA search tool nhmmer. Using default settings in nhmmer, this yields a roughly 10-fold acceleration with small loss of sensitivity on benchmarks.


Help; print a brief reminder of command line usage and all available options.


Assert that 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 information, and for codes for some less common formats, see main documentation. The string <s> is case-insensitive (fasta or FASTA both work).

Bin length. The binary file depends on a data structure called the FM index, which organizes a permuted copy of the sequence in bins of length <n>. Longer bin length will lead to smaller files (because data is captured about each bin) and possibly slower query time. The default is 256. Much more than 512 may lead to notable reduction in speed.

Suffix array sample rate. The FM index structure also samples from the underlying suffix array for the sequence database. More frequent sampling (smaller value for <n>) will yield larger file size and faster search (until file size becomes large enough to cause I/O to be a bottleneck). The default value is 8. Must be a power of 2.

The input sequence is broken into blocks of size <n> million letters. An FM index is built for each block, rather than building an FM index for the entire sequence database. Default is 50. Larger blocks do not seem to yield substantial speed increase.


See hmmer(1) for a 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 (


Copyright (C) 2020 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 (


Nov 2020 HMMER 3.3.2