Mercurial > repos > bgruening > augustus

annotate test-data/extrinsic.truncated.cfg @ 9:bd0e53f3a891 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
author iuc
date Fri, 04 Oct 2024 11:32:08 +0000
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b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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1 ==# extrinsic information configuration file for AUGUSTUS
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2 #
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3 # protein hints
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4 # include with --extrinsicCfgFile=filename
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5 # date: 16.10.2007
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6 # Mario Stanke (mstanke@gwdg.de)
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7
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8
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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9 # source of extrinsic information:
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10 # M manual anchor (required)
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11 # P protein database hit
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12 # E EST/cDNA database hit
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13 # C combined est/protein database hit
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14 # D Dialign
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15 # R retroposed genes
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16 # T transMapped refSeqs
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17 # W wiggle track coverage info from RNA-Seq
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18
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19 [SOURCES]
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20 M RM E W
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22 #
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23 # individual_liability: Only unsatisfiable hints are disregarded. By default this flag is not set
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24 # and the whole hint group is disregarded when one hint in it is unsatisfiable.
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25 # 1group1gene: Try to predict a single gene that covers all hints of a given group. This is relevant for
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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26 # hint groups with gaps, e.g. when two ESTs, say 5' and 3', from the same clone align nearby.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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27 #
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28 [SOURCE-PARAMETERS]
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29
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30
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31 # feature bonus malus gradelevelcolumns
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32 # r+/r-
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33 #
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34 # the gradelevel colums have the following format for each source
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35 # sourcecharacter numscoreclasses boundary ... boundary gradequot ... gradequot
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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36 #
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37
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38 [GENERAL]
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39 start 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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40 stop 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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41 tss 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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42 tts 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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43 ass 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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44 dss 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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45 exonpart 1 .992 M 1 1e+100 RM 1 1 E 1 1 W 1 1.005
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46 exon 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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47 intronpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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48 intron 1 .8 M 1 1e+100 RM 1 1 E 1 1000 W 1 1
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49 CDSpart 1 1 0.985 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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50 CDS 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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51 UTRpart 1 1 .973 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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52 UTR 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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53 irpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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54 nonexonpart 1 1 M 1 1e+100 RM 1 1.01 E 1 1 W 1 1
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55 genicpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
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56
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57 #
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58 # Explanation:
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59 #
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60 # The gff/gtf file containint the hints must contain somewhere in the last
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61 # column an entry source=?, where ? is one of the source characters listed in
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62 # the line after [SOURCES] above. You can use different sources when you have
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63 # hints of different reliability of the same type, e.g. exon hints from ESTs
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64 # and exon hints from evolutionary conservation information.
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65 #
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66 # In the [GENERAL] section the entries second column specify a bonus for obeying
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67 # a hint and the entry in the third column specify a malus (penalty) for
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68 # predicting a feature that is not supported by any hint. The bonus and the
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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69 # malus is a factor that is multiplied to the posterior probability of gene
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70 # structueres.
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71 # Example:
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72 # CDS 1000 0.7 ....
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73 # means that, when AUGUSTUS is searching for the most likely gene structure,
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74 # every gene structure that has a CDS exactly as given in a hint gets
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75 # a bonus factor of 1000. Also, for every CDS that is not supported the
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76 # probability of the gene structure gets a malus of 0.7. Increase the bonus to
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77 # make AUGUSTUS obey more hints, decrease the malus to make AUGUSTUS predict few
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78 # features that are not supported by hints. The malus helps increasing
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79 # specificity, e.g. when the exons predicted by AUGUSTUS are suspicious because
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80 # there is no evidence from ESTs, mRNAs, protein databases, sequence
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81 # conservation, transMapped expressed sequences.
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82 # Setting the malus to 1.0 disables those penalties. Setting the bonus to 1.0
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83 # disables the boni.
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84 #
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85 # start: translation start (start codon), specifies an interval that contains
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86 # the start codon. The interval can be larger than 3bp, in which case
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87 # every ATG in the interval gets a bonus. The highest bonus is given
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88 # to ATGs in the middle of the interval, the bonus fades off towards the ends.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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89 # stop: translation end (stop codon), see 'start'
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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90 # tss: transcription start site, see 'start'
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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91 # tts: transcription termination site, see 'start'
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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92 # ass: acceptor (3') splice site, the last intron position
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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93 # dss: donor (5') splice site, the first intron position
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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94 # exonpart: part of an exon in the biological sense. The bonus applies only
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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95 # to exons that contain the interval from the hint. Just
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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96 # overlapping means no bonus at all. The malus applies to every
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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97 # base of an exon. Therefore the malus for an exon is exponential
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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98 # in the length of an exon: malus=exonpartmalus^length.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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99 # Therefore the malus should be close to 1, e.g. 0.99.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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100 # exon: exon in the biological sense. Only exons that exactly match the
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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101 # hint get a bonus. Exception: The exons that contain the start
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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102 # codon and stop codon. This malus applies to a complete exon
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103 # independent of its length.
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104 # intronpart: introns both between coding and non-coding exons. The bonus
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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105 # applies to every intronic base in the interval of the hint.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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106 # intron: An intron gets the bonus if and only if it is exactly as in the hint.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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107 # CDSpart: part of the coding part of an exon. (CDS = coding sequence)
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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108 # CDS: coding part of an exon with exact boundaries. For internal exons
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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109 # of a multi exon gene this is identical to the biological
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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110 # boundaries of the exon. For the first and the last coding exon
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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111 # the boundaries are the boundaries of the coding sequence (start, stop).
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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112 # UTR: exact boundaries of a UTR exon or the untranslated part of a
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113 # partially coding exon.
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114 # UTRpart: The hint interval must be included in the UTR part of an exon.
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115 # irpart: The bonus applies to every base of the intergenic region. If UTR
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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116 # prediction is turned on (--UTR=on) then UTR is considered
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117 # genic. If you choose against the usual meaning the bonus of
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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118 # irparts to be much smaller than 1 in the configuration file you
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119 # can force AUGUSTUS to not predict an intergenic region in the
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120 # specified interval. This is useful if you want to tell AUGUSTUS
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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121 # that two distant exons belong to the same gene, when AUGUSTUS
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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122 # tends to split that gene into smaller genes.
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123 # nonexonpart: intergenic region or intron. The bonus applies to very non-exon
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124 # base that overlaps with the interval from the hint. It is
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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125 # geometric in the length of that overlap, so choose it close to
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126 # 1.0. This is useful as a weak kind of masking, e.g. when it is
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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127 # unlikely that a retroposed gene contains a coding region but you
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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128 # do not want to completely forbid exons.
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129 # genicpart: everything that is not intergenic region, i.e. intron or exon or UTR if
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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130 # applicable. The bonus applies to every genic base that overlaps with the
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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131 # interval from the hint. This can be used in particular to make Augustus
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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132 # predict one gene between positions a and b if a and b are experimentally
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133 # confirmed to be part of the same gene, e.g. through ESTs from the same clone.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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134 # alias: nonirpart
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135 #
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136 # Any hints of types dss, intron, exon, CDS, UTR that (implicitly) suggest a donor splice
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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137 # site allow AUGUSTUS to predict a donor splice site that has a GC instead of the much more common GT.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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138 # AUGUSTUS does not predict a GC donor splice site unless there is a hint for one.
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139 #
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140 # Starting in column number 4 you can tell AUGUSTUS how to modify the bonus
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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141 # depending on the source of the hint and the score of the hint.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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142 # The score of the hints is specified in the 6th column of the hint gff/gtf.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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143 # If the score is used at all, the score is not used directly through some
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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144 # conversion formula but by distinguishing different classes of scores, e.g. low
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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145 # score, medium score, high score. The format is the following:
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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146 # First, you specify the source character, then the number of classes (say n), then you
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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147 # specify the score boundaries that separate the classes (n-1 thresholds) and then you specify
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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148 # for each score class the multiplicative modifier to the bonus (n factors).
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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149 #
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150 # Examples:
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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151 #
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152 # M 1 1e+100
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153 # means for the manual hint there is only one score class, the bonus for this
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154 # type of hint is multiplied by 10^100. This practically forces AUGUSTUS to obey
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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155 # all manual hints.
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156 #
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157 # T 2 1.5 1 5e29
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158 # For the transMap hints distinguish 2 classes. Those with a score below 1.5 and
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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159 # with a score above 1.5. The bonus if the lower score hints is unchanged and
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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160 # the bonus of the higher score hints is multiplied by 5x10^29.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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161 #
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162 # D 8 1.5 2.5 3.5 4.5 5.5 6.5 7.5 0.58 0.4 0.2 2.9 0.87 0.44 0.31 7.3
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163 # Use 8 score classes for the DIALIGN hints. DIALIGN hints give a score, a strand and
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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164 # reading frame information for CDSpart hints. The strand and reading frame are often correct but not
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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165 # often enough to rely on them. To account for that I generated hints for all
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166 # 6 combinations of a strand and reading frame and then used 2x2x2=8 different
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167 # score classes:
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168 # {low score, high score} x {DIALIGN strand, opposite strand} x {DIALIGN reading frame, other reading frame}
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169 # This example shows that scores don't have to be monotonous. A higher score
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170 # does not have to mean a higher bonus. They are merely a way of classifying the
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171 # hints into categories as you wish. In particular, you could get the effect of
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172 # having different sources by having just hints of one source and then distinguishing
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173 # more scores classes.
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174 #
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175 #
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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176 # Future plans:
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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177 # - Add fuzzy intron hints. Introns get a bonus only when they approximately
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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178 # have the same boundaries as in the hint.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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179 # - Make the splice site hints fuzzy also. Allow a hint interval that contains a
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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180 # likely splice site, as opposed to only an individual position.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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181 # - Write a program that automatically optimizes the boni and mali given an
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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182 # annotated test set of genes and hints for that set of sequences.
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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183