2.2g hmmcalibrate - calibrate HMM search statistics S. Eddy hmm hmmcalibrate hmmcalibrate perl "hmmcalibrate" 0 description description of hmmcalibrate -100 perl "" 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. toto perl "" 1000 hmmfile HMM file perl " $value" 2 hmmer_HMM perl 1 new_hmmfile perl "" 10 "$hmmfile" hmmer_HMM perl 1 expert_options Expert Options 1 fixed Fix the length of the random sequences to n (--fixed n) perl ($value) ? " --fixed $value" : "" 1 Fix the length of the random sequences to n, where n is a positive (and reasonably sized) integer. The default is instead to generate sequences with a variety of different lengths, controlled by a Gaussian (normal) distribution. histfile histogram of the scores(--histfile f) perl ($value) ? " --histfile $value" : "" 1 Save a histogram of the scores and the fitted theoretical curve to file f mean mean length (--mean x) perl ($value) ? " --mean $value" : "" 1 Set the mean length of the synthetic sequences to x, where x is a positive real number. The default is 350. num number of synthetic sequences(--num n) perl ($value) ? " --num $value" : "" 1 Set the number of synthetic sequences to n, where n is a positive integer. If n is less than about 1000, Higher numbers of n will give better determined EVD parameters. The default is 5000; it was empirically chosen as a tradeoff between accuracy and computation time. sd standard deviation (--sd x) perl ($value) ? " -sd $value" : "" 1 Set the standard deviation of the synthetic sequence length distribution to x, where x is a positive real number. The default is 350. Note that the Gaussian is left-truncated so that no sequences have lengths <= 0. seed random seed (--seed n) perl ($value) ? " --seed $value" : "" 1 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.