1 -bash-3.2$ /sw/opt/hmmer3/bin/jackhmmer -h
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2 # jackhmmer :: iteratively search a protein sequence against a protein database
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3 # HMMER 3.0 (March 2010); http://hmmer.org/
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4 # Copyright (C) 2010 Howard Hughes Medical Institute.
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5 # Freely distributed under the GNU General Public License (GPLv3).
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6 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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7 Usage: jackhmmer [-options] <query seqfile> <target seqdb>
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9 where basic options are:
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10 -h : show brief help on version and usage
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11 -N <n> : set maximum number of iterations to <n> [5] (n>0)
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13 options directing output:
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14 -o <f> : direct output to file <f>, not stdout
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15 -A <f> : save multiple alignment of hits to file <s>
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16 --tblout <f> : save parseable table of per-sequence hits to file <s>
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17 --domtblout <f> : save parseable table of per-domain hits to file <s>
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18 --chkhmm <f> : save HMM checkpoints to files <s>-<iteration>.hmm
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19 --chkali <f> : save alignment checkpoints to files <s>-<iteration>.sto
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20 --acc : prefer accessions over names in output
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21 --noali : don't output alignments, so output is smaller
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22 --notextw : unlimit ASCII text output line width
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23 --textw <n> : set max width of ASCII text output lines [120] (n>=120)
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25 options controlling scoring system in first iteration:
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26 --popen <x> : gap open probability [0.02] (0<=x<0.5)
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27 --pextend <x> : gap extend probability [0.4] (0<=x<1)
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28 --mxfile <f> : substitution score matrix [default: BLOSUM62]
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30 options controlling reporting thresholds:
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31 -E <x> : report sequences <= this E-value threshold in output [10.0] (x>0)
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32 -T <x> : report sequences >= this score threshold in output
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33 --domE <x> : report domains <= this E-value threshold in output [10.0] (x>0)
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34 --domT <x> : report domains >= this score cutoff in output
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36 options controlling significance thresholds for inclusion in next round:
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37 --incE <x> : consider sequences <= this E-value threshold as significant
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38 --incT <x> : consider sequences >= this score threshold as significant
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39 --incdomE <x> : consider domains <= this E-value threshold as significant
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40 --incdomT <x> : consider domains >= this score threshold as significant
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42 options controlling acceleration heuristics:
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43 --max : Turn all heuristic filters off (less speed, more power)
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44 --F1 <x> : Stage 1 (MSV) threshold: promote hits w/ P <= F1 [0.02]
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45 --F2 <x> : Stage 2 (Vit) threshold: promote hits w/ P <= F2 [1e-3]
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46 --F3 <x> : Stage 3 (Fwd) threshold: promote hits w/ P <= F3 [1e-5]
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47 --nobias : turn off composition bias filter
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49 options controlling model construction after first iteration:
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50 --fast : assign cols w/ >= symfrac residues as consensus
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51 --hand : manual construction (requires reference annotation)
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52 --symfrac <x> : sets sym fraction controlling --fast construction
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53 --fragthresh <x> : if L < x<L>, tag sequence as a fragment
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55 options controlling relative weights in models after first iteration:
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56 --wpb : Henikoff position-based weights [default]
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57 --wgsc : Gerstein/Sonnhammer/Chothia tree weights
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58 --wblosum : Henikoff simple filter weights
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59 --wnone : don't do any relative weighting; set all to 1
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60 --wid <x> : for --wblosum: set identity cutoff [0.62] (0<=x<=1)
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62 options controlling effective seq number in models after first iteration:
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63 --eent : adjust eff seq # to achieve relative entropy target [default]
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64 --eclust : eff seq # is # of single linkage clusters
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65 --enone : no effective seq # weighting: just use nseq
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66 --eset <x> : set eff seq # for all models to <x>
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67 --ere <x> : for --eent: set minimum rel entropy/position to <x>
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68 --esigma <x> : for --eent: set sigma param to <x> [45.0]
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69 --eid <x> : for --eclust: set fractional identity cutoff to <x> [0.62]
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71 Options controlling E value calibration:
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72 --EmL <n> : length of sequences for MSV Gumbel mu fit [200] (n>0)
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73 --EmN <n> : number of sequences for MSV Gumbel mu fit [200] (n>0)
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74 --EvL <n> : length of sequences for Viterbi Gumbel mu fit [200] (n>0)
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75 --EvN <n> : number of sequences for Viterbi Gumbel mu fit [200] (n>0)
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76 --EfL <n> : length of sequences for Forward exp tail tau fit [100] (n>0)
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77 --EfN <n> : number of sequences for Forward exp tail tau fit [200] (n>0)
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78 --Eft <x> : tail mass for Forward exponential tail tau fit [0.04] (0<x<1)
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80 Other expert options:
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81 --nonull2 : turn off biased composition score corrections
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82 -Z <x> : set # of comparisons done, for E-value calculation
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83 --domZ <x> : set # of significant seqs, for domain E-value calculation
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84 --seed <n> : set RNG seed to <n> (if 0: one-time arbitrary seed) [42]
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85 --qformat <s> : assert query <seqfile> is in format <s>: no autodetection
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86 --tformat <s> : assert target <seqdb> is in format <s>>: no autodetection
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87 --cpu <n> : number of parallel CPU workers to use for multithreads
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