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HMMER
User's Guide
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Dept. of Genetics |
WashU |
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Sequencing Center |
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Eddy lab |
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HMMER |
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Subsections
hmmemit
[options] hmmfile
hmmemit reads an HMM file from hmmfile
and generates a number of sequences from it. This can be useful for various
applications in which one needs a simulation of sequences consistent with
a sequence family consensus. By default, hmmemit generates 10 sequences
and outputs them in FASTA (unaligned) format.
- [-a ] Write the generated
sequences in an aligned format (SELEX) rather than FASTA.
- [-h ] Print brief
help; includes version number and summary of all options, including expert
options.
- [-n <n> ] Generate <n> sequences. Default is 10.
- [-o <f> ] Save the sequences
to file <f> rather than writing them to stdout.
- [-q ] Quiet; suppress all output
except for the sequences themselves. Useful for piping or directing the
output.
- [-seed <n> ] Set the random seed to <n>, where <n> is
a positive integer. The default is to use time() to generate a different
seed for each run, which means that two different runs of hmmemit on the
same HMM will give slightly different results. You can use this option
to generate reproducible results.
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Direct comments and questions to <eddy@genetics.wustl.edu>