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comparison 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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1 <tool id="trnascan" name="tRNAscan" version="0.2.1">
2 <description>tRNA Scan</description>
3 <requirements>
4 <requirement type="package" version="1.3.1">tRNAscan-SE</requirement>
5 </requirements>
6 <command interpreter="python">
7 tRNAscan.py $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -o $tabular_output $inputfile $fasta_output
8 </command>
9 <inputs>
10 <param name="inputfile" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/>
11 <param name="organism" type="select" format="text">
12 <label>Select Organsim</label>
13 <option value="-G">general tRNA model</option>
14 <option value="-B">Bacterial</option>
15 <option value="-A">Archaeal</option>
16 <option value="-O">Mitochondrial/Chloroplast</option>
17 </param>
18 <param name="mode" type="select" format="text">
19 <label>Select Mode</label>
20 <option value=""> Default</option>
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>
27 <param name='disablePseudo' type='boolean' label='Disable pseudo gene checking' truevalue='-D' falsevalue='' > </param>
28 <param name='showPrimSecondOpt' type='boolean' label='Show primary and secondary structure components to Cove scores' truevalue="-H" falsevalue=''></param>
29 <param name='showCodons' type='boolean' label='Show codons instead of tRNA anticodons' truevalue='-N' falsevalue=''></param>
30 </inputs>
31 <outputs>
32 <data format="tabular" name="tabular_output"/>
33 <data format="fasta" name="fasta_output"/>
34 </outputs>
35 <tests>
36 <test>
37 </test>
38 </tests>
39
40 <help>
41
42 .. class:: warningmark
43
44 **TIP** This tool requires *fasta* format.
45
46 -----
47
48 **What it does**
49
50 tRNAscan-SE was designed to make rapid, sensitive searches of genomic
51 sequence feasible using the selectivity of the Cove analysis package.
52 We have optimized search sensitivity with eukaryote cytoplasmic and
53 eubacterial sequences, but it may be applied more broadly with a
54 slight reduction in sensitivity .
55 http://lowelab.ucsc.edu/tRNAscan-SE/
56
57 -----
58
59 **Organisim**
60
61 - use general tRNA model:
62
63 This option selects the general tRNA covariance model that was trained
64 on tRNAs from all three phylogenetic domains (archaea, bacteria, and
65 eukarya). This mode can be used when analyzing a mixed collection of
66 sequences from more than one phylogenetic domain, with only slight
67 loss of sensitivity and selectivity. The original publication
68 describing this program and tRNAscan-SE version 1.0 used this general
69 tRNA model exclusively. If you wish to compare scores to those found
70 in the paper or scans using v1.0, use this option. Use of this option
71 is compatible with all other search mode options described in this
72 section.
73
74 - search for bacterial tRNAs
75
76 This option selects the bacterial covariace model for tRNA analysis,
77 and loosens the search parameters for EufindtRNA to improve detection
78 of bacterial tRNAs. Use of this mode with bacterial sequences
79 will also improve bounds prediction of the 3' end (the terminal CAA
80 triplet).
81
82 - search for archaeal tRNAs
83
84 This option selects an archaeal-specific covariance model for tRNA
85 analysis, as well as slightly loosening the EufindtRNA search
86 cutoffs.
87
88 - search for organellar (mitochondrial/chloroplast) tRNAs
89
90 This parameter bypasses the fast first-pass scanners that are poor at
91 detecting organellar tRNAs and runs Cove analysis only. Since true
92 organellar tRNAs have been found to have Cove scores between 15 and 20
93 bits, the search cutoff is lowered from 20 to 15 bits. Also,
94 pseudogene checking is disabled since it is only applicable to
95 eukaryotic cytoplasmic tRNA pseudogenes. Since Cove-only mode is
96 used, searches will be very slow (see -C option below) relative to the
97 default mode.
98
99 ------
100
101 **Mode**
102
103 - search using Cove analysis only (max sensitivity, slow)
104
105 Directs tRNAscan-SE to analyze sequences using Cove analysis only.
106 This option allows a slightly more sensitive search than the default
107 tRNAscan + EufindtRNA -> Cove mode, but is much slower (by approx. 250
108 to 3,000 fold). Output format and other program defaults are
109 otherwise identical to the normal analysis.
110
111 - search using Eukaryotic tRNA finder (EufindtRNA) only:
112
113 This option runs EufindtRNA alone to search for tRNAs. Since Cove is
114 not being used as a secondary filter to remove false positives, this
115 run mode defaults to "Normal" parameters which more closely
116 approximates the sensitivity and selectivity of the original algorithm
117 describe by Pavesi and colleagues.
118
119 - search using tRNAscan only (defaults to strict search params)
120
121 Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This
122 mode will cause tRNAscan to default to using "strict" parameters
123 (similar to tRNAscan version 1.3 operation). This mode of operation
124 is faster (about 3-5 times faster than default mode analysis), but
125 will result in approximately 0.2 to 0.6 false positive tRNAs per Mbp,
126 decreased sensitivity, and less reliable prediction of anticodons,
127 tRNA isotype, and introns.
128
129 -----
130
131 **disable pseudogene checking**
132
133 Manually disable checking tRNAs for poor primary or secondary
134 structure scores often indicative of eukaryotic pseudogenes. This
135 will slightly speed the program and may be necessary for non-eukaryotic
136 sequences that are flagged as possible pseudogenes but are known to be
137 functional tRNAs.
138
139 -----
140
141 **Show both primary and secondary structure score components to covariance model bit scores**
142
143 This option displays the breakdown of the two components of the
144 covariance model bit score. Since tRNA pseudogenes often have one
145 very low component (good secondary structure but poor primary sequence
146 similarity to the tRNA model, or vice versa), this information may be
147 useful in deciding whether a low-scoring tRNA is likely to be a
148 pseudogene. The heuristic pseudogene detection filter uses this
149 information to flag possible pseudogenes -- use this option to see why
150 a hit is marked as a possible pseudogene. The user may wish to
151 examine score breakdowns from known tRNAs in the organism of interest
152 to get a frame of reference.
153
154 -----
155
156 **Show codons instead of tRNA anticodons**
157
158 This option causes tRNAscan-SE to output a tRNA's corresponding codon
159 in place of its anticodon.
160
161 -----
162
163 **Example**
164
165 * input::
166
167 -Genome Sequence
168
169 CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
170 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
171 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
172 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
173 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
174 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
175 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
176 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
177 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
178 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
179 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
180 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
181 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
182 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
183 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
184 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
185 .....
186 - organisim : Mixed (general tRNA model)
187 - mode : Default
188 - disable pseudogene checking : not checked
189 - Show both primary and secondary structure score components to covariance model bit scores : not checked
190 - Show codons instead of tRNA anticodons : not checked
191
192 * output::
193
194 Sequence tRNA Bounds tRNA Anti Intron Bounds Cove Hit
195 Name tRNA # Begin End Type Codon Begin End Score Origin
196 -------- ------ ---- ------ ---- ----- ----- ---- ------ ------
197 CELF22B7 1 12619 12738 Leu CAA 12657 12692 55.12 Bo
198 CELF22B7 2 19480 19561 Ser AGA 0 0 66.90 Bo
199 CELF22B7 3 26367 26439 Phe GAA 0 0 73.88 Bo
200 CELF22B7 4 26992 26920 Phe GAA 0 0 73.88 Bo
201 CELF22B7 5 23765 23694 Pro CGG 0 0 60.58 Bo
202
203
204
205 -------
206
207 **References**
208
209 Todd M. Lowe and Sean R. Eddy
210 tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964
211 doi:10.1093/nar/25.5.0955
212
213 </help>
214
215 </tool>