/var/lib/mobyle/programs/sirna.xml is in mobyle-programs 5.1.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 | <?xml version="1.0" encoding="ISO-8859-1"?>
<!-- XML Authors: Corinne Maufrais and Nicolas Joly, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>sirna</name>
<package>
<name>EMBOSS</name>
<version>6.3.1</version>
<doc>
<title>EMBOSS</title>
<description>
<text lang="en">European Molecular Biology Open Software Suite</text>
</description>
<authors>Rice,P. Longden,I. and Bleasby, A.</authors>
<reference>EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby, A. Trends in Genetics 16, (6) pp276--277</reference>
<sourcelink>http://emboss.sourceforge.net/download</sourcelink>
<homepagelink>http://emboss.sourceforge.net</homepagelink>
</doc>
</package>
<doc>
<title>sirna</title>
<description>
<text lang="en">Finds siRNA duplexes in mRNA</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/sirna.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>sequence:nucleic:composition</category>
<command>sirna</command>
</head>
<parameters>
<paragraph>
<name>e_input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_sequence</name>
<prompt lang="en">sequence option</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>EMBL</dataFormat>
<dataFormat>FASTA</dataFormat>
<dataFormat>GCG</dataFormat>
<dataFormat>GENBANK</dataFormat>
<dataFormat>NBRF</dataFormat>
<dataFormat>CODATA</dataFormat>
<dataFormat>RAW</dataFormat>
<dataFormat>SWISSPROT</dataFormat>
<dataFormat>GFF</dataFormat>
<card>1,n</card>
</type>
<format>
<code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
<paragraph>
<name>e_seqinsection</name>
<prompt lang="en">Sequence input options</prompt>
<parameters>
<parameter>
<name>e_poliii</name>
<prompt lang="en">Select probes for pol iii expression vectors</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -poliii")[ bool(value) ]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">This option allows you to select only the 21 base probes that start with a purine and so can be expressed from Pol III expression vectors. This is the NARN(17)YNN pattern that has been suggested by Tuschl et al.</text>
</comment>
</parameter>
<parameter>
<name>e_aa</name>
<prompt lang="en">Select only regions that start with aa</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -aa")[ bool(value) ]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">This option allows you to select only those 23 base regions that start with AA. If this option is not selected then regions that start with AA will be favoured by giving them a higher score, but regions that do not start with AA will also be reported.</text>
</comment>
</parameter>
<parameter>
<name>e_tt</name>
<prompt lang="en">Select only regions that end with tt</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -tt")[ bool(value) ]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">This option allows you to select only those 23 base regions that end with TT. If this option is not selected then regions that end with TT will be favoured by giving them a higher score, but regions that do not end with TT will also be reported.</text>
</comment>
</parameter>
<parameter>
<name>e_polybase</name>
<prompt lang="en">Allow regions with 4 repeats of a base</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nopolybase", "")[ bool(value) ]</code>
</format>
<argpos>5</argpos>
<comment>
<text lang="en">If this option is FALSE then only those 23 base regions that have no repeat of 4 or more of any bases in a row will be reported. No regions will ever be reported that have 4 or more G's in a row.</text>
</comment>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_outfile</name>
<prompt lang="en">Name of the report file</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>sirna.report</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>6</argpos>
<comment>
<text lang="en">The output is a table of the forward and reverse parts of the 21 base siRNA duplex. Both the forward and reverse sequences are written 5' to 3', ready to be ordered. The last two bases have been replaced by 'dTdT'. The starting position of the 23 base region and the %GC content is also given. If you wish to see the complete 23 base sequence, then either look at the sequence in the other output file, or use the qualifier '-context' which will display the 23 bases of the forward sequence in this report with the first two bases in brackets. These first two bases do not form part of the siRNA probe to be ordered.</text>
</comment>
</parameter>
<parameter>
<name>e_rformat_outfile</name>
<prompt lang="en">Choose the report output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>TABLE</value>
</vdef>
<vlist>
<velem>
<value>DASGFF</value>
<label>Dasgff</label>
</velem>
<velem>
<value>DBMOTIF</value>
<label>Dbmotif</label>
</velem>
<velem>
<value>DIFFSEQ</value>
<label>Diffseq</label>
</velem>
<velem>
<value>EMBL</value>
<label>Embl</label>
</velem>
<velem>
<value>EXCEL</value>
<label>Excel</label>
</velem>
<velem>
<value>FEATTABLE</value>
<label>Feattable</label>
</velem>
<velem>
<value>GENBANK</value>
<label>Genbank</label>
</velem>
<velem>
<value>GFF</value>
<label>Gff</label>
</velem>
<velem>
<value>LISTFILE</value>
<label>Listfile</label>
</velem>
<velem>
<value>MOTIF</value>
<label>Motif</label>
</velem>
<velem>
<value>NAMETABLE</value>
<label>Nametable</label>
</velem>
<velem>
<value>CODATA</value>
<label>Codata</label>
</velem>
<velem>
<value>REGIONS</value>
<label>Regions</label>
</velem>
<velem>
<value>SEQTABLE</value>
<label>Seqtable</label>
</velem>
<velem>
<value>SIMPLE</value>
<label>Simple</label>
</velem>
<velem>
<value>SRS</value>
<label>Srs</label>
</velem>
<velem>
<value>SWISS</value>
<label>Swiss</label>
</velem>
<velem>
<value>TABLE</value>
<label>Table</label>
</velem>
<velem>
<value>TAGSEQ</value>
<label>Tagseq</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -rformat=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>7</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
<dataFormat>
<ref param="e_rformat_outfile">
</ref>
</dataFormat>
</type>
<precond>
<code proglang="python">e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']</code>
</precond>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
<parameter>
<name>e_outseq</name>
<prompt lang="en">Name of the output sequence file (e_outseq)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>sirna.e_outseq</value>
</vdef>
<format>
<code proglang="python">("" , " -outseq=" + str(value))[value is not None]</code>
</format>
<argpos>8</argpos>
<comment>
<text lang="en">This is a file of the sequences of the 23 base regions that the siRNAs are selected from. You may use it to do searches of mRNA databases (e.g. REFSEQ) to confirm that the probes are unique to the gene you wish to use it on.</text>
</comment>
</parameter>
<parameter>
<name>e_osformat_outseq</name>
<prompt lang="en">Choose the sequence output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>FASTA</value>
</vdef>
<vlist>
<velem>
<value>EMBL</value>
<label>Embl</label>
</velem>
<velem>
<value>FASTA</value>
<label>Fasta</label>
</velem>
<velem>
<value>GCG</value>
<label>Gcg</label>
</velem>
<velem>
<value>GENBANK</value>
<label>Genbank</label>
</velem>
<velem>
<value>NBRF</value>
<label>Nbrf</label>
</velem>
<velem>
<value>CODATA</value>
<label>Codata</label>
</velem>
<velem>
<value>RAW</value>
<label>Raw</label>
</velem>
<velem>
<value>SWISSPROT</value>
<label>Swissprot</label>
</velem>
<velem>
<value>GFF</value>
<label>Gff</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -osformat=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>9</argpos>
</parameter>
<parameter isout="1">
<name>e_outseq_out</name>
<prompt lang="en">outseq_out option</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>
<ref param="e_osformat_outseq">
</ref>
</dataFormat>
</type>
<filenames>
<code proglang="python">e_outseq</code>
</filenames>
</parameter>
<parameter>
<name>e_context</name>
<prompt lang="en">Show the two bases before the output 21 base probe</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -context")[ bool(value) ]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">The output report file gives the sequences of the 21 base siRNA regions ready to be ordered. This does not give you an indication of the 2 bases before the 21 bases. It is often interesting to see which of the suggested possible probe regions have an 'AA' in front of them (i.e. it is useful to see which of the 23 base regions start with an 'AA'). This option displays the whole 23 bases of the region with the first two bases in brackets, e.g. '(AA)' to give you some context for the probe region. YOU SHOULD NOT INCLUDE THE TWO BASES IN BRACKETS WHEN YOU PLACE AN ORDER FOR THE PROBES.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter ishidden="1">
<name>auto</name>
<prompt lang="en">Turn off any prompting</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">" -auto -stdout"</code>
</format>
<argpos>11</argpos>
</parameter>
</parameters>
</program>
|