2
|
1 <tool id="trnascan" name="tRNAscan" version="0.2.2">
|
1
|
2 <description>tRNA Scan</description>
|
|
3 <requirements>
|
|
4 <requirement type="package" version="1.3.1">tRNAscan-SE</requirement>
|
2
|
5 <requirement type="python-module">biopython</requirement>
|
1
|
6 </requirements>
|
|
7 <command interpreter="python">
|
|
8 tRNAscan.py $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -o $tabular_output $inputfile $fasta_output
|
|
9 </command>
|
|
10 <inputs>
|
|
11 <param name="inputfile" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/>
|
2
|
12 <param name="organism" type="select" label="Select Organism">
|
|
13 <option value="">Eukaryotic</option>
|
1
|
14 <option value="-G">general tRNA model</option>
|
|
15 <option value="-B">Bacterial</option>
|
|
16 <option value="-A">Archaeal</option>
|
|
17 <option value="-O">Mitochondrial/Chloroplast</option>
|
|
18 </param>
|
2
|
19 <param name="mode" type="select" label="Select Mode">
|
|
20 <option value="">Default</option>
|
1
|
21 <option value="-C">Covariance model analysis only (slow)</option>
|
|
22 <option value="-T">tRNAscan only</option>
|
|
23 <option value="-E">EufindtRNA only</option>
|
|
24 <option value="--infernal">Infernal cm analysis (max sensitivity, very slow)</option>
|
|
25 <option value="--newscan">Infernal and new cm models</option>
|
|
26 </param>
|
2
|
27 <param name="disablePseudo" type="boolean" label="Disable pseudogene checking" truevalue="-D" falsevalue="" />
|
|
28 <param name="showPrimSecondOpt" type="boolean" label="Show primary and secondary structure components to Cove scores" truevalue="-H" falsevalue="" />
|
|
29 <param name="showCodons" type="boolean" label="Show codons instead of tRNA anticodons" truevalue="-N" falsevalue="" />
|
1
|
30 </inputs>
|
|
31 <outputs>
|
2
|
32 <data format="tabular" name="tabular_output" label="${tool.name} on ${on_string}: tabular" />
|
|
33 <data format="fasta" name="fasta_output" label="${tool.name} on ${on_string}: fasta" />
|
1
|
34 </outputs>
|
|
35 <tests>
|
|
36 <test>
|
|
37 </test>
|
|
38 </tests>
|
2
|
39 <help>
|
1
|
40
|
|
41 .. class:: warningmark
|
|
42
|
|
43 **TIP** This tool requires *fasta* format.
|
|
44
|
|
45 -----
|
|
46
|
|
47 **What it does**
|
|
48
|
|
49 tRNAscan-SE was designed to make rapid, sensitive searches of genomic
|
|
50 sequence feasible using the selectivity of the Cove analysis package.
|
|
51 We have optimized search sensitivity with eukaryote cytoplasmic and
|
|
52 eubacterial sequences, but it may be applied more broadly with a
|
|
53 slight reduction in sensitivity .
|
|
54 http://lowelab.ucsc.edu/tRNAscan-SE/
|
|
55
|
|
56 -----
|
|
57
|
2
|
58 **Organism**
|
|
59
|
|
60 - search for eukaryotic cytoplasmic tRNAs:
|
|
61
|
|
62 This is the default.
|
1
|
63
|
|
64 - use general tRNA model:
|
|
65
|
|
66 This option selects the general tRNA covariance model that was trained
|
2
|
67 on tRNAs from all three phylogenetic domains (Archaea, Bacteria, and
|
|
68 Eukarya). This mode can be used when analyzing a mixed collection of
|
1
|
69 sequences from more than one phylogenetic domain, with only slight
|
2
|
70 loss of sensitivity and selectivity. The original publication
|
1
|
71 describing this program and tRNAscan-SE version 1.0 used this general
|
2
|
72 tRNA model exclusively. If you wish to compare scores to those found
|
|
73 in the paper or scans using v1.0, use this option. Use of this option
|
1
|
74 is compatible with all other search mode options described in this
|
|
75 section.
|
|
76
|
|
77 - search for bacterial tRNAs
|
|
78
|
2
|
79 This option selects the bacterial covariance model for tRNA analysis,
|
1
|
80 and loosens the search parameters for EufindtRNA to improve detection
|
2
|
81 of bacterial tRNAs. Use of this mode with bacterial sequences
|
1
|
82 will also improve bounds prediction of the 3' end (the terminal CAA
|
|
83 triplet).
|
|
84
|
|
85 - search for archaeal tRNAs
|
|
86
|
|
87 This option selects an archaeal-specific covariance model for tRNA
|
|
88 analysis, as well as slightly loosening the EufindtRNA search
|
|
89 cutoffs.
|
|
90
|
|
91 - search for organellar (mitochondrial/chloroplast) tRNAs
|
|
92
|
|
93 This parameter bypasses the fast first-pass scanners that are poor at
|
2
|
94 detecting organellar tRNAs and runs Cove analysis only. Since true
|
1
|
95 organellar tRNAs have been found to have Cove scores between 15 and 20
|
2
|
96 bits, the search cutoff is lowered from 20 to 15 bits. Also,
|
1
|
97 pseudogene checking is disabled since it is only applicable to
|
2
|
98 eukaryotic cytoplasmic tRNA pseudogenes. Since Cove-only mode is
|
1
|
99 used, searches will be very slow (see -C option below) relative to the
|
|
100 default mode.
|
|
101
|
|
102 ------
|
|
103
|
|
104 **Mode**
|
|
105
|
|
106 - search using Cove analysis only (max sensitivity, slow)
|
|
107
|
|
108 Directs tRNAscan-SE to analyze sequences using Cove analysis only.
|
|
109 This option allows a slightly more sensitive search than the default
|
|
110 tRNAscan + EufindtRNA -> Cove mode, but is much slower (by approx. 250
|
2
|
111 to 3,000 fold). Output format and other program defaults are
|
1
|
112 otherwise identical to the normal analysis.
|
|
113
|
|
114 - search using Eukaryotic tRNA finder (EufindtRNA) only:
|
|
115
|
2
|
116 This option runs EufindtRNA alone to search for tRNAs. Since Cove is
|
1
|
117 not being used as a secondary filter to remove false positives, this
|
|
118 run mode defaults to "Normal" parameters which more closely
|
|
119 approximates the sensitivity and selectivity of the original algorithm
|
|
120 describe by Pavesi and colleagues.
|
|
121
|
2
|
122 - search using tRNAscan only (defaults to strict search parameters)
|
1
|
123
|
2
|
124 Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This
|
1
|
125 mode will cause tRNAscan to default to using "strict" parameters
|
2
|
126 (similar to tRNAscan version 1.3 operation). This mode of operation
|
1
|
127 is faster (about 3-5 times faster than default mode analysis), but
|
|
128 will result in approximately 0.2 to 0.6 false positive tRNAs per Mbp,
|
|
129 decreased sensitivity, and less reliable prediction of anticodons,
|
|
130 tRNA isotype, and introns.
|
|
131
|
|
132 -----
|
|
133
|
|
134 **disable pseudogene checking**
|
|
135
|
|
136 Manually disable checking tRNAs for poor primary or secondary
|
2
|
137 structure scores often indicative of eukaryotic pseudogenes. This
|
1
|
138 will slightly speed the program and may be necessary for non-eukaryotic
|
|
139 sequences that are flagged as possible pseudogenes but are known to be
|
|
140 functional tRNAs.
|
|
141
|
|
142 -----
|
|
143
|
|
144 **Show both primary and secondary structure score components to covariance model bit scores**
|
|
145
|
|
146 This option displays the breakdown of the two components of the
|
2
|
147 covariance model bit score. Since tRNA pseudogenes often have one
|
1
|
148 very low component (good secondary structure but poor primary sequence
|
|
149 similarity to the tRNA model, or vice versa), this information may be
|
|
150 useful in deciding whether a low-scoring tRNA is likely to be a
|
2
|
151 pseudogene. The heuristic pseudogene detection filter uses this
|
1
|
152 information to flag possible pseudogenes -- use this option to see why
|
2
|
153 a hit is marked as a possible pseudogene. The user may wish to
|
1
|
154 examine score breakdowns from known tRNAs in the organism of interest
|
|
155 to get a frame of reference.
|
|
156
|
|
157 -----
|
|
158
|
|
159 **Show codons instead of tRNA anticodons**
|
|
160
|
|
161 This option causes tRNAscan-SE to output a tRNA's corresponding codon
|
|
162 in place of its anticodon.
|
|
163
|
|
164 -----
|
|
165
|
|
166 **Example**
|
|
167
|
|
168 * input::
|
|
169
|
|
170 -Genome Sequence
|
|
171
|
|
172 CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
|
|
173 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
|
|
174 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
|
|
175 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
|
|
176 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
|
|
177 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
|
|
178 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
|
|
179 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
|
|
180 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
|
|
181 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
|
|
182 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
|
|
183 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
|
|
184 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
|
|
185 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
|
|
186 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
|
|
187 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
|
|
188 .....
|
2
|
189 - organism : Mixed (general tRNA model)
|
1
|
190 - mode : Default
|
|
191 - disable pseudogene checking : not checked
|
|
192 - Show both primary and secondary structure score components to covariance model bit scores : not checked
|
|
193 - Show codons instead of tRNA anticodons : not checked
|
|
194
|
|
195 * output::
|
|
196
|
|
197 Sequence tRNA Bounds tRNA Anti Intron Bounds Cove Hit
|
|
198 Name tRNA # Begin End Type Codon Begin End Score Origin
|
|
199 -------- ------ ---- ------ ---- ----- ----- ---- ------ ------
|
|
200 CELF22B7 1 12619 12738 Leu CAA 12657 12692 55.12 Bo
|
|
201 CELF22B7 2 19480 19561 Ser AGA 0 0 66.90 Bo
|
|
202 CELF22B7 3 26367 26439 Phe GAA 0 0 73.88 Bo
|
|
203 CELF22B7 4 26992 26920 Phe GAA 0 0 73.88 Bo
|
|
204 CELF22B7 5 23765 23694 Pro CGG 0 0 60.58 Bo
|
|
205
|
|
206
|
|
207
|
|
208 -------
|
|
209
|
|
210 **References**
|
|
211
|
|
212 Todd M. Lowe and Sean R. Eddy
|
|
213 tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964
|
|
214 doi:10.1093/nar/25.5.0955
|
|
215
|
2
|
216 </help>
|
1
|
217 </tool>
|