/var/lib/mobyle/programs/getorf.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 | <?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>getorf</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>getorf</title>
<description>
<text lang="en">Finds and extracts open reading frames (ORFs)</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/getorf.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>sequence:nucleic:gene_finding</category>
<command>getorf</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>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_table</name>
<prompt lang="en">Genetic codes</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Standard</label>
</velem>
<velem>
<value>1</value>
<label>Standard (with alternative initiation codons)</label>
</velem>
<velem>
<value>2</value>
<label>Vertebrate mitochondrial</label>
</velem>
<velem>
<value>3</value>
<label>Yeast mitochondrial</label>
</velem>
<velem>
<value>4</value>
<label>Mold, protozoan, coelenterate mitochondrial and mycoplasma/spiroplasma</label>
</velem>
<velem>
<value>5</value>
<label>Invertebrate mitochondrial</label>
</velem>
<velem>
<value>6</value>
<label>Ciliate macronuclear and dasycladacean</label>
</velem>
<velem>
<value>9</value>
<label>Echinoderm mitochondrial</label>
</velem>
<velem>
<value>10</value>
<label>Euplotid nuclear</label>
</velem>
<velem>
<value>11</value>
<label>Bacterial</label>
</velem>
<velem>
<value>12</value>
<label>Alternative yeast nuclear</label>
</velem>
<velem>
<value>13</value>
<label>Ascidian mitochondrial</label>
</velem>
<velem>
<value>14</value>
<label>Flatworm mitochondrial</label>
</velem>
<velem>
<value>15</value>
<label>Blepharisma macronuclear</label>
</velem>
<velem>
<value>16</value>
<label>Chlorophycean mitochondrial</label>
</velem>
<velem>
<value>21</value>
<label>Trematode mitochondrial</label>
</velem>
<velem>
<value>22</value>
<label>Scenedesmus obliquus</label>
</velem>
<velem>
<value>23</value>
<label>Thraustochytrium mitochondrial</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -table=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>e_minsize</name>
<prompt lang="en">Minimum nucleotide size of orf to report</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>30</value>
</vdef>
<format>
<code proglang="python">("", " -minsize=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>e_maxsize</name>
<prompt lang="en">Maximum nucleotide size of orf to report</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1000000</value>
</vdef>
<format>
<code proglang="python">("", " -maxsize=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>4</argpos>
</parameter>
<parameter>
<name>e_find</name>
<prompt lang="en">Type of sequence to output</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Translation of regions between stop codons</label>
</velem>
<velem>
<value>1</value>
<label>Translation of regions between start and stop codons</label>
</velem>
<velem>
<value>2</value>
<label>Nucleic sequences between stop codons</label>
</velem>
<velem>
<value>3</value>
<label>Nucleic sequences between start and stop codons</label>
</velem>
<velem>
<value>4</value>
<label>Nucleotides flanking start codons</label>
</velem>
<velem>
<value>5</value>
<label>Nucleotides flanking initial stop codons</label>
</velem>
<velem>
<value>6</value>
<label>Nucleotides flanking ending stop codons</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -find=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>5</argpos>
<comment>
<text lang="en">This is a small menu of possible output options. The first four options are to select either the protein translation or the original nucleic acid sequence of the open reading frame. There are two possible definitions of an open reading frame: it can either be a region that is free of STOP codons or a region that begins with a START codon and ends with a STOP codon. The last three options are probably only of interest to people who wish to investigate the statistical properties of the regions around potential START or STOP codons. The last option assumes that ORF lengths are calculated between two STOP codons.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_advanced</name>
<prompt lang="en">Advanced section</prompt>
<parameters>
<parameter>
<name>e_methionine</name>
<prompt lang="en">Change initial start codons to methionine</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nomethionine", "")[ bool(value) ]</code>
</format>
<argpos>6</argpos>
<comment>
<text lang="en">START codons at the beginning of protein products will usually code for Methionine, despite what the codon will code for when it is internal to a protein. This qualifier sets all such START codons to code for Methionine by default.</text>
</comment>
</parameter>
<parameter>
<name>e_circular</name>
<prompt lang="en">Is the sequence circular</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -circular")[ bool(value) ]</code>
</format>
<argpos>7</argpos>
</parameter>
<parameter>
<name>e_reverse</name>
<prompt lang="en">Find orfs in the reverse sequence</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noreverse", "")[ bool(value) ]</code>
</format>
<argpos>8</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to find ORFs in the reverse complement of the sequence.</text>
</comment>
</parameter>
<parameter>
<name>e_flanking</name>
<prompt lang="en">Number of flanking nucleotides to report</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>100</value>
</vdef>
<format>
<code proglang="python">("", " -flanking=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">If you have chosen one of the options of the type of sequence to find that gives the flanking sequence around a STOP or START codon, this allows you to set the number of nucleotides either side of that codon to output. If the region of flanking nucleotides crosses the start or end of the sequence, no output is given for this codon.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_outseq</name>
<prompt lang="en">Name of the output sequence file (e_outseq)</prompt>
<type>
<biotype>Protein</biotype>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>outseq.orf</value>
</vdef>
<format>
<code proglang="python">("" , " -outseq=" + str(value))[value is not None]</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter>
<name>e_osformat_outseq</name>
<prompt lang="en">Choose the sequence output format</prompt>
<type>
<biotype>Protein</biotype>
<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>11</argpos>
</parameter>
<parameter isout="1">
<name>e_outseq_out</name>
<prompt lang="en">outseq_out option</prompt>
<type>
<biotype>Protein</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>
<ref param="e_osformat_outseq">
</ref>
</dataFormat>
</type>
<filenames>
<code proglang="python">e_outseq</code>
</filenames>
</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>12</argpos>
</parameter>
</parameters>
</program>
|