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HMMER
User's Guide
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Subsections
hmmcalibrate
[options] hmmfile
hmmcalibrate reads an HMM file from hmmfile,
scores a large number of synthesized random sequences with it, fits an
extreme value distribution (EVD) to the histogram of those scores, and
re-saves hmmfile now including the EVD parameters.
hmmcalibrate may take
several minutes (or longer) to run. While it is running, a temporary file
called hmmfile.xxx is generated in your working directory. If you abort
hmmcalibrate prematurely (ctrl-C, for instance), your original hmmfile
will be untouched, and you should delete the hmmfile.xxx temporary file.
- [-h ] Print brief help; includes version number and summary of
all options, including expert options.
- [-fixed <n> ] Fix the
length of the random sequences to <n>, where <n> is a positive (and reasonably
sized) integer. The default is instead to generate sequences with a variety
of different lengths, controlled by a Gaussian (normal) distribution.
- [-histfile <f> ] Save a histogram of the scores and the fitted theoretical
curve to file <f>.
- [-mean <x> ] Set the mean length of the synthetic sequences
to <x>, where <x> is a positive real number. The default is 350.
- [-num <n> ] Set
the number of synthetic sequences to <n>, where <n> is a positive integer.
If <n> is less than about 1000, the fit to the EVD may fail. Higher numbers
of <n> will give better determined EVD parameters. The default is 5000;
it was empirically chosen as a tradeoff between accuracy and computation
time.
- [-sd <x> ] Set the standard deviation of the synthetic sequence length
distribution to <x>, where <x> is a positive real number. The default is 350.
Note that the Gaussian is left-truncated so that no sequences have lengths
<= 0.
- [-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 hmmcalibrate on the same HMM will
give slightly different results. You can use this option to generate reproducible
results for different hmmcalibrate runs on the same HMM.
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Direct comments and questions to <eddy@genetics.wustl.edu>