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ehmmcalibrate |
% ehmmcalibrate globin.hmm -seed 1079460101 -auto |
Go to the output files for this example
Standard (Mandatory) qualifiers: [-infile] infile HMM file [-outfile] outfile Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -cpu integer Number of CPUs -fixed integer Length fix for random sequences -mean float Mean length of synthetic sequences -num integer Number of synthetic sequences -pvm boolean Run on parallel virtual machines -sd float Standard deviation of syntheic sequences -seed integer Random seed -histogramfile outfile Name for histogram file Associated qualifiers: "-outfile" associated qualifiers -odirectory2 string Output directory "-histogramfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-infile] (Parameter 1) |
HMM file | Input file | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.ehmmcalibrate |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
-cpu | Number of CPUs | Any integer value | 0 |
-fixed | Length fix for random sequences | Integer 0 or more | 0 |
-mean | Mean length of synthetic sequences | Any numeric value | 350. |
-num | Number of synthetic sequences | Any integer value | 5000 |
-pvm | Run on parallel virtual machines | Boolean value Yes/No | No |
-sd | Standard deviation of syntheic sequences | Any numeric value | 350. |
-seed | Random seed | Integer 0 or more | 0 |
-histogramfile | Name for histogram file | Output file |
HMM file: globin.hmm Length distribution mean: 350 Length distribution s.d.: 350 Number of samples: 5000 random seed: 1079460101 histogram(s) saved to: globin.out2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM : globins50 mu : -7.978981 lambda : 0.646464 max : 4.780000 // |
HMM: globins50 score obs exp (one = represents 17 sequences) ----- --- --- -19 2 0|= -18 2 0|= -17 4 0|= -16 8 0|= -15 25 0|== -14 60 0|==== -13 62 0|==== -12 163 4|*========= -11 282 120|=======*========= -10 646 597|===================================*== -9 940 1092|======================================================== * -8 997 1125|==========================================================* -7 733 845|============================================ * -6 475 536|============================ * -5 286 310|================= * -4 153 171|========= * -3 80 92|=====* -2 34 49|==* -1 27 25|=* 0 12 13|* 1 7 7|* 2 1 3|* 3 0 1|* 4 1 1|* % Statistical details of theoretical EVD fit: mu = -7.9790 lambda = 0.6465 chi-sq statistic = 47.1730 P(chi-square) = 1.421e-07 // |
HMMER2.0 NAME globins50 LENG 146 ALPH Amino RF no CS no MAP yes COM ehmmbuild ../../data/hmm/globins50.msf globin.hmm -auto COM ehmmcalibrate globin.hmm -seed 1079460101 -auto NSEQ 50 DATE Fri Jul 15 12:00:00 2005 CKSUM 5854 XT -8455 -4 0 * -8455 -4 0 * NULT -4 -8455 NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 EVD -7.978981 0.646464 HMM A C D E F G H I K L M N P Q R S T V W Y m->m m->i m->d i->m i->i d->m d->d b->m m->e -93 * -4000 1 -1967 -2271 -4498 -4217 -3055 1639 -3307 -2518 -3920 -2945 2068 -3352 193 -3569 -3796 257 -2222 2801 -3514 -3205 1 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -1093 -8180 2 -1670 -1776 -76 -2279 1025 -3037 3194 232 -52 1914 -955 -2245 -3102 -1004 -2223 -2065 -1610 -1207 -2178 -1775 2 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -8273 -8175 3 -1713 -1550 -3992 -3365 801 -3249 -2111 -1027 -2974 762 -736 -2876 -3301 -2606 -2796 1725 1747 269 3309 -1618 3 - 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* * * * * * * * * * * * * * * * * * * * - * * * * * * * -8273 0 // |
Program name | Description |
---|---|
ealistat | Statistics for multiple alignment files |
ehmmalign | Align sequences with an HMM |
ehmmbuild | Build HMM |
ehmmconvert | Convert between HMM formats |
ehmmemit | Extract HMM sequences |
ehmmfetch | Extract HMM from a database |
ehmmindex | Index an HMM database |
ehmmpfam | Align single sequence with an HMM |
ehmmsearch | Search sequence database with an HMM |
Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.
Please report all bugs in the EMBOSS version to the EMBOSS bug team, not to the original author.