Mercurial > repos > bjoern-gruening > trna_prediction
comparison tools/tRNAscan.xml @ 0:b46d3df3eb9e
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author | bjoern-gruening |
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date | Wed, 11 Jan 2012 05:57:32 -0500 |
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1 <tool id="trnascan" name="tRNAscan" version="0.1"> | |
2 <description>tRNA Scan</description> | |
3 <command >tRNAscan-SE $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -d -Q -y -q -b -o $output $inputfile > /dev/null </command> | |
4 <inputs> | |
5 <param name="inputfile" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/> | |
6 <param name="organism" type="select" format="text"> | |
7 <label>Select Organsim</label> | |
8 <option value="-G">general tRNA model</option> | |
9 <option value="-B">Bacterial</option> | |
10 <option value="-A">Archaeal</option> | |
11 <option value="-O">Mito/Chloroplast </option> | |
12 </param> | |
13 <param name="mode" type="select" format="text"> | |
14 <label>Select Mode</label> | |
15 <option value=""> Default</option> | |
16 <option value="-C"> Cove only (very slow)</option> | |
17 <option value="-T"> tRNAscan only</option> | |
18 <option value="-E "> EufindtRNA only</option> | |
19 </param> | |
20 <param name='disablePseudo' type='boolean' label='Disable pseudo gene checking' truevalue='-D' falsevalue='' > </param> | |
21 <param name='showPrimSecondOpt' type='boolean' label='Show primary and secondary structure components to Cove scores ' truevalue="-H" falsevalue=''></param> | |
22 <param name='showCodons' type='boolean' label='Show codons instead of tRNA anticodons' truevalue='-N' falsevalue=''></param> | |
23 </inputs> | |
24 <outputs> | |
25 <data format="tabular" name="output" /> | |
26 </outputs> | |
27 <tests> | |
28 <test> | |
29 <param name="inputfile" ftype="fasta" value='trna/trnaTestData.fa' /> | |
30 <param name="organism" value='general tRNA model' /> | |
31 <param name="mode" value="" /> | |
32 <param name='disablePseudo' value=''/> | |
33 <param name='showPrimSecondOpt' value="" /> | |
34 <param name='showCodons' value='' /> | |
35 <output name="output" file='trna/trnaTestOutput.dat'/> | |
36 </test> | |
37 </tests> | |
38 | |
39 <help> | |
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 | |
58 **Organisim** | |
59 | |
60 - use general tRNA model: | |
61 | |
62 This option selects the general tRNA covariance model that was trained | |
63 on tRNAs from all three phylogenetic domains (archaea, bacteria, and | |
64 eukarya). This mode can be used when analyzing a mixed collection of | |
65 sequences from more than one phylogenetic domain, with only slight | |
66 loss of sensitivity and selectivity. The original publication | |
67 describing this program and tRNAscan-SE version 1.0 used this general | |
68 tRNA model exclusively. If you wish to compare scores to those found | |
69 in the paper or scans using v1.0, use this option. Use of this option | |
70 is compatible with all other search mode options described in this | |
71 section. | |
72 | |
73 - search for bacterial tRNAs | |
74 | |
75 This option selects the bacterial covariace model for tRNA analysis, | |
76 and loosens the search parameters for EufindtRNA to improve detection | |
77 of bacterial tRNAs. Use of this mode with bacterial sequences | |
78 will also improve bounds prediction of the 3' end (the terminal CAA | |
79 triplet). | |
80 | |
81 - search for archaeal tRNAs | |
82 | |
83 This option selects an archaeal-specific covariance model for tRNA | |
84 analysis, as well as slightly loosening the EufindtRNA search | |
85 cutoffs. | |
86 | |
87 - search for organellar (mitochondrial/chloroplast) tRNAs | |
88 | |
89 This parameter bypasses the fast first-pass scanners that are poor at | |
90 detecting organellar tRNAs and runs Cove analysis only. Since true | |
91 organellar tRNAs have been found to have Cove scores between 15 and 20 | |
92 bits, the search cutoff is lowered from 20 to 15 bits. Also, | |
93 pseudogene checking is disabled since it is only applicable to | |
94 eukaryotic cytoplasmic tRNA pseudogenes. Since Cove-only mode is | |
95 used, searches will be very slow (see -C option below) relative to the | |
96 default mode. | |
97 | |
98 ------ | |
99 | |
100 **Mode** | |
101 | |
102 - search using Cove analysis only (max sensitivity, slow) | |
103 | |
104 Directs tRNAscan-SE to analyze sequences using Cove analysis only. | |
105 This option allows a slightly more sensitive search than the default | |
106 tRNAscan + EufindtRNA -> Cove mode, but is much slower (by approx. 250 | |
107 to 3,000 fold). Output format and other program defaults are | |
108 otherwise identical to the normal analysis. | |
109 | |
110 - search using Eukaryotic tRNA finder (EufindtRNA) only: | |
111 | |
112 This option runs EufindtRNA alone to search for tRNAs. Since Cove is | |
113 not being used as a secondary filter to remove false positives, this | |
114 run mode defaults to "Normal" parameters which more closely | |
115 approximates the sensitivity and selectivity of the original algorithm | |
116 describe by Pavesi and colleagues. | |
117 | |
118 - search using tRNAscan only (defaults to strict search params) | |
119 | |
120 Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This | |
121 mode will cause tRNAscan to default to using "strict" parameters | |
122 (similar to tRNAscan version 1.3 operation). This mode of operation | |
123 is faster (about 3-5 times faster than default mode analysis), but | |
124 will result in approximately 0.2 to 0.6 false positive tRNAs per Mbp, | |
125 decreased sensitivity, and less reliable prediction of anticodons, | |
126 tRNA isotype, and introns. | |
127 | |
128 ----- | |
129 | |
130 **disable pseudogene checking** | |
131 | |
132 Manually disable checking tRNAs for poor primary or secondary | |
133 structure scores often indicative of eukaryotic pseudogenes. This | |
134 will slightly speed the program and may be necessary for non-eukaryotic | |
135 sequences that are flagged as possible pseudogenes but are known to be | |
136 functional tRNAs. | |
137 | |
138 ----- | |
139 | |
140 **Show both primary and secondary structure score components to covariance model bit scores** | |
141 | |
142 This option displays the breakdown of the two components of the | |
143 covariance model bit score. Since tRNA pseudogenes often have one | |
144 very low component (good secondary structure but poor primary sequence | |
145 similarity to the tRNA model, or vice versa), this information may be | |
146 useful in deciding whether a low-scoring tRNA is likely to be a | |
147 pseudogene. The heuristic pseudogene detection filter uses this | |
148 information to flag possible pseudogenes -- use this option to see why | |
149 a hit is marked as a possible pseudogene. The user may wish to | |
150 examine score breakdowns from known tRNAs in the organism of interest | |
151 to get a frame of reference. | |
152 | |
153 ----- | |
154 | |
155 **Show codons instead of tRNA anticodons** | |
156 | |
157 This option causes tRNAscan-SE to output a tRNA's corresponding codon | |
158 in place of its anticodon. | |
159 | |
160 ----- | |
161 | |
162 **Example** | |
163 | |
164 * input:: | |
165 | |
166 -Genome Sequence | |
167 | |
168 CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7 | |
169 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT | |
170 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT | |
171 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT | |
172 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC | |
173 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA | |
174 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG | |
175 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA | |
176 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA | |
177 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC | |
178 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA | |
179 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC | |
180 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC | |
181 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA | |
182 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC | |
183 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT | |
184 ..... | |
185 - organisim : Mixed (general tRNA model) | |
186 - mode : Default | |
187 - disable pseudogene checking : not checked | |
188 - Show both primary and secondary structure score components to covariance model bit scores : not checked | |
189 - Show codons instead of tRNA anticodons : not checked | |
190 | |
191 * output:: | |
192 | |
193 Sequence tRNA Bounds tRNA Anti Intron Bounds Cove Hit | |
194 Name tRNA # Begin End Type Codon Begin End Score Origin | |
195 -------- ------ ---- ------ ---- ----- ----- ---- ------ ------ | |
196 CELF22B7 1 12619 12738 Leu CAA 12657 12692 55.12 Bo | |
197 CELF22B7 2 19480 19561 Ser AGA 0 0 66.90 Bo | |
198 CELF22B7 3 26367 26439 Phe GAA 0 0 73.88 Bo | |
199 CELF22B7 4 26992 26920 Phe GAA 0 0 73.88 Bo | |
200 CELF22B7 5 23765 23694 Pro CGG 0 0 60.58 Bo | |
201 | |
202 | |
203 | |
204 ------- | |
205 | |
206 **References** | |
207 | |
208 Todd M. Lowe and Sean R. Eddy | |
209 tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964 | |
210 doi:10.1093/nar/25.5.0955 | |
211 | |
212 </help> | |
213 | |
214 </tool> |