SYNOPSISmakehmmerdb [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.Usingdefaultsettingsin nhmmer, this yields a roughly 10-fold acceleration with small loss of sensitivity on benchmarks. (This method has been extensively tested, but should still be treated as somewhat experimental.)
Help; print a brief reminder of command line usage and all available
- --informat <s>
Assert that the sequence database file is in format
Accepted formats include
The default is to autodetect the format of the file.
- --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 in bins
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
- --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 (smaller value for
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.
- --block_size <n>
The input sequence is broken into blocks of size
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.
Copyright (C) 2015 Howard Hughes Medical Institute. Freely distributed under the GNU General Public License (GPLv3).
For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page ().
Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org