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hmmpress - Online in the Cloud

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

This is the command hmmpress 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



hmmpress - prepare an HMM database for hmmscan


hmmpress [options] <hmmfile>


Starting from a profile database <hmmfile> in standard HMMER3 format, construct binary
compressed datafiles for hmmscan. The hmmpress step is required for hmmscan to work.

Four files are created: <hmmfile>.h3m, <hmmfile>.h3i, <hmmfile>.h3f, and <hmmfile>.h3p.
The <hmmfile>.h3m file contains the profile HMMs and their annotation in a binary format.
The <hmmfile>.h3i file is an SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file
contains precomputed data structures for the fast heuristic filter (the MSV filter). The
<hmmfile>.h3p file contains precomputed data structures for the rest of each profile.

<hmmfile> may not be '-' (dash); running hmmpress on a standard input stream rather than a
file is not allowed.


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

-f Force; overwrites any previous hmmpress'ed datafiles. The default is to bitch about
any existing files and ask you to delete them first.

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