bionic (1) makehmmerdb.1.gz

Provided by: hmmer_3.1b2+dfsg-5ubuntu1_amd64 bug

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 (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