EnglishFrenchSpanish

Ad


OnWorks favicon

makehmmerdb - Online in the Cloud

Run makehmmerdb in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command makehmmerdb that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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.

Use makehmmerdb online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    OpenFOAM
    OpenFOAM
    OpenFOAM - The Open Source CFD Toolbox.
    OpenFOAM is a generic, programmable
    software tool for Computational Fluid
    Dynamics (CFD). For more information,
    see: - ...
    Download OpenFOAM
  • 2
    PostInstallerF
    PostInstallerF
    PostInstallerF will install all the
    software that Fedora Linux and others
    doesn't include by default, after
    running Fedora for the first time. Its
    easy for...
    Download PostInstallerF
  • 3
    strace
    strace
    The strace project has been moved to
    https://strace.io. strace is a
    diagnostic, debugging and instructional
    userspace tracer for Linux. It is used
    to monitor a...
    Download strace
  • 4
    JasperReports Library
    JasperReports Library
    JasperReports Library is the
    world's most popular open source
    business intelligence and reporting
    engine. It is entirely written in Java
    and it is able to ...
    Download JasperReports Library
  • 5
    Numerical Python
    Numerical Python
    NEWS: NumPy 1.11.2 is the last release
    that will be made on sourceforge. Wheels
    for Windows, Mac, and Linux as well as
    archived source distributions can be fou...
    Download Numerical Python
  • 6
    CMU Sphinx
    CMU Sphinx
    CMUSphinx is a speaker-independent large
    vocabulary continuous speech recognizer
    released under BSD style license. It is
    also a collection of open source tools ...
    Download CMU Sphinx
  • 7
    Old Feren OS Repositories
    Old Feren OS Repositories
    This was the Official Repository for
    Feren OS. To add the latest one, run
    this command: (16.04-based) echo
    "deb ...
    Download Old Feren OS Repositories
  • More »

Linux commands

Ad