annotate tRNAscan.xml @ 1:65d282ef088e draft

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author bjoern-gruening
date Tue, 19 Mar 2013 16:56:25 -0400
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children 0fef99b5f63f
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1 <tool id="trnascan" name="tRNAscan" version="0.2.1">
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2 <description>tRNA Scan</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 </requirements>
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6 <command interpreter="python">
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7 tRNAscan.py $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -o $tabular_output $inputfile $fasta_output
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8 </command>
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9 <inputs>
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10 <param name="inputfile" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/>
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11 <param name="organism" type="select" format="text">
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12 <label>Select Organsim</label>
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13 <option value="-G">general tRNA model</option>
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14 <option value="-B">Bacterial</option>
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15 <option value="-A">Archaeal</option>
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16 <option value="-O">Mitochondrial/Chloroplast</option>
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17 </param>
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18 <param name="mode" type="select" format="text">
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19 <label>Select Mode</label>
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20 <option value=""> Default</option>
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21 <option value="-C">Covariance model analysis only (slow)</option>
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22 <option value="-T">tRNAscan only</option>
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23 <option value="-E">EufindtRNA only</option>
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24 <option value="--infernal">Infernal cm analysis (max sensitivity, very slow)</option>
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25 <option value="--newscan">Infernal and new cm models</option>
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26 </param>
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27 <param name='disablePseudo' type='boolean' label='Disable pseudo gene checking' truevalue='-D' falsevalue='' > </param>
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28 <param name='showPrimSecondOpt' type='boolean' label='Show primary and secondary structure components to Cove scores' truevalue="-H" falsevalue=''></param>
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29 <param name='showCodons' type='boolean' label='Show codons instead of tRNA anticodons' truevalue='-N' falsevalue=''></param>
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30 </inputs>
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31 <outputs>
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32 <data format="tabular" name="tabular_output"/>
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33 <data format="fasta" name="fasta_output"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 </test>
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38 </tests>
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39
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40 <help>
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41
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42 .. class:: warningmark
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43
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44 **TIP** This tool requires *fasta* format.
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45
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46 -----
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47
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48 **What it does**
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49
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50 tRNAscan-SE was designed to make rapid, sensitive searches of genomic
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51 sequence feasible using the selectivity of the Cove analysis package.
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52 We have optimized search sensitivity with eukaryote cytoplasmic and
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53 eubacterial sequences, but it may be applied more broadly with a
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54 slight reduction in sensitivity .
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55 http://lowelab.ucsc.edu/tRNAscan-SE/
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56
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57 -----
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58
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59 **Organisim**
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60
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61 - use general tRNA model:
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62
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63 This option selects the general tRNA covariance model that was trained
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64 on tRNAs from all three phylogenetic domains (archaea, bacteria, and
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65 eukarya). This mode can be used when analyzing a mixed collection of
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66 sequences from more than one phylogenetic domain, with only slight
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67 loss of sensitivity and selectivity. The original publication
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68 describing this program and tRNAscan-SE version 1.0 used this general
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69 tRNA model exclusively. If you wish to compare scores to those found
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70 in the paper or scans using v1.0, use this option. Use of this option
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71 is compatible with all other search mode options described in this
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72 section.
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73
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74 - search for bacterial tRNAs
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75
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76 This option selects the bacterial covariace model for tRNA analysis,
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77 and loosens the search parameters for EufindtRNA to improve detection
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78 of bacterial tRNAs. Use of this mode with bacterial sequences
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79 will also improve bounds prediction of the 3' end (the terminal CAA
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80 triplet).
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81
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82 - search for archaeal tRNAs
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83
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84 This option selects an archaeal-specific covariance model for tRNA
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85 analysis, as well as slightly loosening the EufindtRNA search
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86 cutoffs.
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87
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88 - search for organellar (mitochondrial/chloroplast) tRNAs
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89
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90 This parameter bypasses the fast first-pass scanners that are poor at
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91 detecting organellar tRNAs and runs Cove analysis only. Since true
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92 organellar tRNAs have been found to have Cove scores between 15 and 20
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93 bits, the search cutoff is lowered from 20 to 15 bits. Also,
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94 pseudogene checking is disabled since it is only applicable to
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95 eukaryotic cytoplasmic tRNA pseudogenes. Since Cove-only mode is
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96 used, searches will be very slow (see -C option below) relative to the
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97 default mode.
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98
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99 ------
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100
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101 **Mode**
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102
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103 - search using Cove analysis only (max sensitivity, slow)
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104
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105 Directs tRNAscan-SE to analyze sequences using Cove analysis only.
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106 This option allows a slightly more sensitive search than the default
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107 tRNAscan + EufindtRNA -> Cove mode, but is much slower (by approx. 250
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108 to 3,000 fold). Output format and other program defaults are
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109 otherwise identical to the normal analysis.
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110
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111 - search using Eukaryotic tRNA finder (EufindtRNA) only:
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112
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113 This option runs EufindtRNA alone to search for tRNAs. Since Cove is
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114 not being used as a secondary filter to remove false positives, this
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115 run mode defaults to "Normal" parameters which more closely
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116 approximates the sensitivity and selectivity of the original algorithm
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117 describe by Pavesi and colleagues.
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118
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119 - search using tRNAscan only (defaults to strict search params)
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120
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121 Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This
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122 mode will cause tRNAscan to default to using "strict" parameters
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123 (similar to tRNAscan version 1.3 operation). This mode of operation
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124 is faster (about 3-5 times faster than default mode analysis), but
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125 will result in approximately 0.2 to 0.6 false positive tRNAs per Mbp,
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126 decreased sensitivity, and less reliable prediction of anticodons,
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127 tRNA isotype, and introns.
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128
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129 -----
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130
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131 **disable pseudogene checking**
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132
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133 Manually disable checking tRNAs for poor primary or secondary
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134 structure scores often indicative of eukaryotic pseudogenes. This
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135 will slightly speed the program and may be necessary for non-eukaryotic
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136 sequences that are flagged as possible pseudogenes but are known to be
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137 functional tRNAs.
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138
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139 -----
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140
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141 **Show both primary and secondary structure score components to covariance model bit scores**
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142
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143 This option displays the breakdown of the two components of the
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144 covariance model bit score. Since tRNA pseudogenes often have one
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145 very low component (good secondary structure but poor primary sequence
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146 similarity to the tRNA model, or vice versa), this information may be
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147 useful in deciding whether a low-scoring tRNA is likely to be a
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148 pseudogene. The heuristic pseudogene detection filter uses this
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149 information to flag possible pseudogenes -- use this option to see why
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150 a hit is marked as a possible pseudogene. The user may wish to
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151 examine score breakdowns from known tRNAs in the organism of interest
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152 to get a frame of reference.
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153
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154 -----
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155
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156 **Show codons instead of tRNA anticodons**
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157
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158 This option causes tRNAscan-SE to output a tRNA's corresponding codon
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159 in place of its anticodon.
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160
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161 -----
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162
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163 **Example**
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164
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165 * input::
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166
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167 -Genome Sequence
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168
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169 CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
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170 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
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171 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
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172 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
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173 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
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174 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
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175 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
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176 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
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177 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
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178 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
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179 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
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180 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
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181 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
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182 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
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183 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
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184 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
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185 .....
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186 - organisim : Mixed (general tRNA model)
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187 - mode : Default
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188 - disable pseudogene checking : not checked
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189 - Show both primary and secondary structure score components to covariance model bit scores : not checked
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190 - Show codons instead of tRNA anticodons : not checked
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191
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192 * output::
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193
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194 Sequence tRNA Bounds tRNA Anti Intron Bounds Cove Hit
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195 Name tRNA # Begin End Type Codon Begin End Score Origin
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196 -------- ------ ---- ------ ---- ----- ----- ---- ------ ------
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197 CELF22B7 1 12619 12738 Leu CAA 12657 12692 55.12 Bo
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198 CELF22B7 2 19480 19561 Ser AGA 0 0 66.90 Bo
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199 CELF22B7 3 26367 26439 Phe GAA 0 0 73.88 Bo
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200 CELF22B7 4 26992 26920 Phe GAA 0 0 73.88 Bo
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201 CELF22B7 5 23765 23694 Pro CGG 0 0 60.58 Bo
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202
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203
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204
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205 -------
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206
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207 **References**
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208
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209 Todd M. Lowe and Sean R. Eddy
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210 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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211 doi:10.1093/nar/25.5.0955
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212
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213 </help>
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214
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215 </tool>