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1 <tool id="aragorn_trna" name="Aragon" version="0.1">
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2 <description>Prediction of tRNAs</description>
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3 <command>aragorn $input > $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="fasta" label="Genome Sequence"/>
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6 </inputs>
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7 <outputs>
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8 <data name="output" format="tabular"/>
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9 </outputs>
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10 <tests>
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11 <test>
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12 </test>
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13 </tests>
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14 <help>
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15
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16 **What it does**
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17
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18 This tool predicts, tRNA (and tmRNA) detection in nucleotide sequences.
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19 http://130.235.46.10/ARAGORN/
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20 -----
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21
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22 **Example**
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23
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24 Suppose you have the following DNA formatted sequences::
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25
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26 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other;
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27 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
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28 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
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29 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
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30 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
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31 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
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32
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33 Running this tool will produce this::
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34 --snip--
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35 87.
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36
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37 c
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38 c
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39 a
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40 g-c
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41 g-c
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42 g-c
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43 c-g
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44 g-c
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45 a-t
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46 t-a ca
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47 t tgacc a
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48 ga a !!!!! g
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49 t ctcg actgg c
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50 g !!!! c tt
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51 g gagc t
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52 aa g g
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53 c-gag
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54 t-a
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55 t-a
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56 c-g
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57 g-c
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58 t c
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59 t a
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60 cac
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61
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62
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63
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64 tRNA-Val(cac)
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65 74 bases, %GC = 58.1
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66 Sequence [6669703,6669776]
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67
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68
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69
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70
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71 tRNA Anticodon Frequency
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72 AAA Phe GAA Phe 1 CAA Leu 1 TAA Leu 1
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73 AGA Ser GGA Ser 1 CGA Ser 2 TGA Ser 1
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74 ACA Cys GCA Cys 2 CCA Trp 2 TCA seC
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75 ATA Tyr GTA Tyr 1 CTA Pyl TTA Stop
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76 AAG Leu GAG Leu 3 CAG Leu 1 TAG Leu 2
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77 AGG Pro GGG Pro 2 CGG Pro 2 TGG Pro 2
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78 ACG Arg 1 GCG Arg 2 CCG Arg 1 TCG Arg
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79 ATG His GTG His 2 CTG Gln 2 TTG Gln 1
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80 AAC Val GAC Val 3 CAC Val 2 TAC Val 1
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81 AGC Ala GGC Ala 2 CGC Ala 3 TGC Ala 1
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82 ACC Gly GCC Gly 5 CCC Gly 1 TCC Gly 2
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83 ATC Asp GTC Asp 3 CTC Glu 2 TTC Glu 2
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84 AAT Ile GAT Ile 3 CAT Met 6 TAT Ile
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85 AGT Thr GGT Thr 2 CGT Thr 1 TGT Thr 2
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86 ACT Ser GCT Ser 1 CCT Arg 1 TCT Arg 1
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87 ATT Asn GTT Asn 3 CTT Lys 3 TTT Lys 2
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88 Ambiguous: 1
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89
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90 tRNA Codon Frequency
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91 TTT Phe TTC Phe 1 TTG Leu 1 TTA Leu 1
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92 TCT Ser TCC Ser 1 TCG Ser 2 TCA Ser 1
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93 TGT Cys TGC Cys 2 TGG Trp 2 TGA seC
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94 TAT Tyr TAC Tyr 1 TAG Pyl TAA Stop
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95 CTT Leu CTC Leu 3 CTG Leu 1 CTA Leu 2
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96 CCT Pro CCC Pro 2 CCG Pro 2 CCA Pro 2
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97 CGT Arg 1 CGC Arg 2 CGG Arg 1 CGA Arg
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98 CAT His CAC His 2 CAG Gln 2 CAA Gln 1
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99 GTT Val GTC Val 3 GTG Val 2 GTA Val 1
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100 GCT Ala GCC Ala 2 GCG Ala 3 GCA Ala 1
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101 GGT Gly GGC Gly 5 GGG Gly 1 GGA Gly 2
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102 GAT Asp GAC Asp 3 GAG Glu 2 GAA Glu 2
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103 ATT Ile ATC Ile 3 ATG Met 6 ATA Ile
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104 ACT Thr ACC Thr 2 ACG Thr 1 ACA Thr 2
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105 AGT Ser AGC Ser 1 AGG Arg 1 AGA Arg 1
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106 AAT Asn AAC Asn 3 AAG Lys 3 AAA Lys 2
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107 Ambiguous: 1
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108
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109 Number of tRNA genes = 86
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110 tRNA GC range = 50.0% to 85.1%
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111 Number of tmRNA genes = 1
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112
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113 -------
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114
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115 **References**
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116
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117 Dean Laslett and Bjorn Canback
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118 ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16
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119 doi:10.1093/nar/gkh152
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120
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121
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122
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123 </help>
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124 </tool>
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