NAME

       makehmmerdb - build a HMMER binary database file from a sequence file

SYNOPSIS

       makehmmerdb [options] <seqfile> <binaryfile>

DESCRIPTION

       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.)

OPTIONS

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

OTHER OPTIONS

       --informat <s>
              Assert  that the sequence database file is in format <s>.  Accepted formats include
              fasta, embl, genbank, ddbj, uniprot, stockholm, pfam, a2m, and afa.  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 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.

       --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
              <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.

       --block_size <n>
              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 ALSO

       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

       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 ().

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org