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1 <tool id="trnascan" name="tRNA prediction" version="0.3">
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2 <description>(tRNAscan)</description>
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3 <requirements>
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4 <requirement type="package" version="1.3.1">tRNAscan-SE</requirement>
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5 <requirement type="package" version="1.61">biopython</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8 <![CDATA[
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9 tRNAscan.py
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10 $organism
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11 $mode
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12 $showPrimSecondOpt
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13 $disablePseudo
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14 $showCodons
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15 -o
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16 $tabular_output
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17 $inputfile
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18 $fasta_output
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="inputfile" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/>
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23 <param name="organism" type="select" label="Select Organism">
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24 <option value="">Eukaryotic</option>
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25 <option value="-G">general tRNA model</option>
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26 <option value="-B">Bacterial</option>
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27 <option value="-A">Archaeal</option>
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28 <option value="-O">Mitochondrial/Chloroplast</option>
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29 </param>
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30 <param name="mode" type="select" label="Select Mode">
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31 <option value="">Default</option>
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32 <option value="-C">Covariance model analysis only (slow)</option>
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33 <option value="-T">tRNAscan only</option>
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34 <option value="-E">EufindtRNA only</option>
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35 <option value="--infernal">Infernal cm analysis (max sensitivity, very slow)</option>
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36 <option value="--newscan">Infernal and new cm models</option>
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37 </param>
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38 <param name="disablePseudo" type="boolean" label="Disable pseudogene checking" truevalue="-D" falsevalue="" />
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39 <param name="showPrimSecondOpt" type="boolean" label="Show primary and secondary structure components to Cove scores" truevalue="-H" falsevalue="" />
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40 <param name="showCodons" type="boolean" label="Show codons instead of tRNA anticodons" truevalue="-N" falsevalue="" />
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41 </inputs>
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42 <outputs>
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43 <data format="tabular" name="tabular_output" label="${tool.name} on ${on_string}: tabular" />
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44 <data format="fasta" name="fasta_output" label="${tool.name} on ${on_string}: fasta" />
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" />
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49 <param name="organism" value="" />
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50 <param name="mode" value="--infernal" />
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51 <param name="disablePseudo" value="" />
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52 <param name="showPrimSecondOpt" value="" />
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53 <param name="showCodons" value="" />
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54 <output name="fasta_output" file="tRNAscan_eukaryotic_infernal.fasta" ftype="fasta" />
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55 <output name="fasta_output" file="tRNAscan_eukaryotic_infernal.tabular" ftype="tabular" />
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56 </test>
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57 </tests>
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58 <help>
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59 <![CDATA[
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60
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61
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62 .. class:: warningmark
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63
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64 **TIP** This tool requires *fasta* formated sequences.
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65
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66 -----
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67
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68 **What it does**
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69
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70 tRNAscan-SE_ was designed to make rapid, sensitive searches of genomic
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71 sequence feasible using the selectivity of the Cove analysis package.
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72 We have optimized search sensitivity with eukaryote cytoplasmic and
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73 eubacterial sequences, but it may be applied more broadly with a
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74 slight reduction in sensitivity.
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75
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76 .. _tRNAscan-SE: http://lowelab.ucsc.edu/tRNAscan-SE/
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77
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78 -----
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79
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80 **Organism**
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81
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82 - search for eukaryotic cytoplasmic tRNAs:
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83
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84 This is the default.
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85
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86 - use general tRNA model:
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87
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88 This option selects the general tRNA covariance model that was trained
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89 on tRNAs from all three phylogenetic domains (Archaea, Bacteria, and
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90 Eukarya). This mode can be used when analyzing a mixed collection of
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91 sequences from more than one phylogenetic domain, with only slight
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92 loss of sensitivity and selectivity. The original publication
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93 describing this program and tRNAscan-SE version 1.0 used this general
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94 tRNA model exclusively. If you wish to compare scores to those found
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95 in the paper or scans using v1.0, use this option. Use of this option
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96 is compatible with all other search mode options described in this
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97 section.
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98
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99 - search for bacterial tRNAs
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100
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101 This option selects the bacterial covariance model for tRNA analysis,
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102 and loosens the search parameters for EufindtRNA to improve detection
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103 of bacterial tRNAs. Use of this mode with bacterial sequences
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104 will also improve bounds prediction of the 3' end (the terminal CAA
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105 triplet).
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106
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107 - search for archaeal tRNAs
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108
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109 This option selects an archaeal-specific covariance model for tRNA
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110 analysis, as well as slightly loosening the EufindtRNA search
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111 cutoffs.
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112
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113 - search for organellar (mitochondrial/chloroplast) tRNAs
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114
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115 This parameter bypasses the fast first-pass scanners that are poor at
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116 detecting organellar tRNAs and runs Cove analysis only. Since true
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117 organellar tRNAs have been found to have Cove scores between 15 and 20
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118 bits, the search cutoff is lowered from 20 to 15 bits. Also,
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119 pseudogene checking is disabled since it is only applicable to
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120 eukaryotic cytoplasmic tRNA pseudogenes. Since Cove-only mode is
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121 used, searches will be very slow (see -C option below) relative to the
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122 default mode.
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123
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124 ------
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125
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126 **Mode**
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127
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128 - search using Cove analysis only (max sensitivity, slow)
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129
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130 Directs tRNAscan-SE to analyze sequences using Cove analysis only.
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131 This option allows a slightly more sensitive search than the default
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132 tRNAscan + EufindtRNA -> Cove mode, but is much slower (by approx. 250
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133 to 3,000 fold). Output format and other program defaults are
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134 otherwise identical to the normal analysis.
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135
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136 - search using Eukaryotic tRNA finder (EufindtRNA) only:
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137
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138 This option runs EufindtRNA alone to search for tRNAs. Since Cove is
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139 not being used as a secondary filter to remove false positives, this
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140 run mode defaults to "Normal" parameters which more closely
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141 approximates the sensitivity and selectivity of the original algorithm
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142 describe by Pavesi and colleagues.
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143
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144 - search using tRNAscan only (defaults to strict search parameters)
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145
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146 Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This
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147 mode will cause tRNAscan to default to using "strict" parameters
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148 (similar to tRNAscan version 1.3 operation). This mode of operation
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149 is faster (about 3-5 times faster than default mode analysis), but
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150 will result in approximately 0.2 to 0.6 false positive tRNAs per Mbp,
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151 decreased sensitivity, and less reliable prediction of anticodons,
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152 tRNA isotype, and introns.
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153
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154 - search using Infernal cm analysis only (max sensitivity, very slow)
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155
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156
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157 - search using Infernal and new cm models instead of Cove
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158
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159
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160 -----
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161
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162 **disable pseudogene checking**
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163
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164 Manually disable checking tRNAs for poor primary or secondary
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165 structure scores often indicative of eukaryotic pseudogenes. This
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166 will slightly speed the program and may be necessary for non-eukaryotic
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167 sequences that are flagged as possible pseudogenes but are known to be
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168 functional tRNAs.
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169
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170 -----
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171
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172 **Show both primary and secondary structure score components to covariance model bit scores**
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173
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174 This option displays the breakdown of the two components of the
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175 covariance model bit score. Since tRNA pseudogenes often have one
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176 very low component (good secondary structure but poor primary sequence
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177 similarity to the tRNA model, or vice versa), this information may be
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178 useful in deciding whether a low-scoring tRNA is likely to be a
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179 pseudogene. The heuristic pseudogene detection filter uses this
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180 information to flag possible pseudogenes -- use this option to see why
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181 a hit is marked as a possible pseudogene. The user may wish to
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182 examine score breakdowns from known tRNAs in the organism of interest
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183 to get a frame of reference.
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184
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185 -----
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186
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187 **Show codons instead of tRNA anticodons**
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188
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189 This option causes tRNAscan-SE to output a tRNA's corresponding codon
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190 in place of its anticodon.
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191
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192 -----
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193
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194 **Example**
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195
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196 * input:
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197
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198 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
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199 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
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200 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
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201 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
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202 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
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203 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
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204 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
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205 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
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206 .....
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207
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208
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209 * output:
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210
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211
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212 ======== ====== ===== ====== ==== ========== ====== ====== ========== ==========
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213 tRNA Bounds Intron Bonds
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214 -------- ------ ---------------- ---- ---------- ---------------- ---------- ----------
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215 Name # tRNA Begin End tRNA Anti Codon Begin End Cove Score Hit Origin
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216 ======== ====== ===== ====== ==== ========== ====== ====== ========== ==========
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217 CELF22B7 1 12619 12738 Leu CAA 12657 12692 55.12 Bo
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218 CELF22B7 2 19480 19561 Ser AGA 0 0 66.90 Bo
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219 CELF22B7 3 26367 26439 Phe GAA 0 0 73.88 Bo
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220 CELF22B7 4 26992 26920 Phe GAA 0 0 73.88 Bo
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221 CELF22B7 5 23765 23694 Pro CGG 0 0 60.58 Bo
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222 ======== ====== ===== ====== ==== ========== ====== ====== ========== ==========
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223
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224
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225 -------
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226
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227 **References**
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228
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229 Todd M. Lowe and Sean R. Eddy
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230
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231 tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964
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232
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233 doi:10.1093/nar/25.5.0955
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235
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236 ]]>
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237 </help>
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238 </tool>
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