1<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> 2<tr bgcolor="#FFFFCC"> 3<th align="left">Qualifier</th> 4<th align="left">Type</th> 5<th align="left">Description</th> 6<th align="left">Allowed values</th> 7<th align="left">Default</th> 8</tr> 9 10<tr bgcolor="#FFFFCC"> 11<th align="left" colspan=5>Standard (Mandatory) qualifiers</th> 12</tr> 13 14<tr bgcolor="#FFFFCC"> 15<td>[-seqall]<br>(Parameter 1)</td> 16<td>seqall</td> 17<td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> 18<td>Readable sequence(s)</td> 19<td><b>Required</b></td> 20</tr> 21 22<tr bgcolor="#FFFFCC"> 23<td>[-outfile]<br>(Parameter 2)</td> 24<td>outfile</td> 25<td>Output file name</td> 26<td>Output file</td> 27<td><i><*></i>.coderet</td> 28</tr> 29 30<tr bgcolor="#FFFFCC"> 31<td>[-cdsoutseq]<br>(Parameter 3)</td> 32<td>seqoutall</td> 33<td>Coding nucleotide output sequence(s) (optional)</td> 34<td>Writeable sequence(s)</td> 35<td><i><*></i>.<i>format</i></td> 36</tr> 37 38<tr bgcolor="#FFFFCC"> 39<td>[-mrnaoutseq]<br>(Parameter 4)</td> 40<td>seqoutall</td> 41<td>Messenger RNA nucleotide output sequence(s) (optional)</td> 42<td>Writeable sequence(s)</td> 43<td><i><*></i>.<i>format</i></td> 44</tr> 45 46<tr bgcolor="#FFFFCC"> 47<td>[-translationoutseq]<br>(Parameter 5)</td> 48<td>seqoutall</td> 49<td>Translated coding protein output sequence(s) (optional)</td> 50<td>Writeable sequence(s)</td> 51<td><i><*></i>.<i>format</i></td> 52</tr> 53 54<tr bgcolor="#FFFFCC"> 55<td>[-restoutseq]<br>(Parameter 6)</td> 56<td>seqoutall</td> 57<td>Non-coding nucleotide output sequence(s) (optional)</td> 58<td>Writeable sequence(s)</td> 59<td><i><*></i>.<i>format</i></td> 60</tr> 61 62<tr bgcolor="#FFFFCC"> 63<th align="left" colspan=5>Additional (Optional) qualifiers</th> 64</tr> 65 66<tr> 67<td colspan=5>(none)</td> 68</tr> 69 70<tr bgcolor="#FFFFCC"> 71<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> 72</tr> 73 74<tr> 75<td colspan=5>(none)</td> 76</tr> 77 78<tr bgcolor="#FFFFCC"> 79<th align="left" colspan=5>Associated qualifiers</th> 80</tr> 81 82<tr bgcolor="#FFFFCC"> 83<td align="left" colspan=5>"-seqall" associated seqall qualifiers 84</td> 85</tr> 86 87<tr bgcolor="#FFFFCC"> 88<td> -sbegin1<br>-sbegin_seqall</td> 89<td>integer</td> 90<td>Start of each sequence to be used</td> 91<td>Any integer value</td> 92<td>0</td> 93</tr> 94 95<tr bgcolor="#FFFFCC"> 96<td> -send1<br>-send_seqall</td> 97<td>integer</td> 98<td>End of each sequence to be used</td> 99<td>Any integer value</td> 100<td>0</td> 101</tr> 102 103<tr bgcolor="#FFFFCC"> 104<td> -sreverse1<br>-sreverse_seqall</td> 105<td>boolean</td> 106<td>Reverse (if DNA)</td> 107<td>Boolean value Yes/No</td> 108<td>N</td> 109</tr> 110 111<tr bgcolor="#FFFFCC"> 112<td> -sask1<br>-sask_seqall</td> 113<td>boolean</td> 114<td>Ask for begin/end/reverse</td> 115<td>Boolean value Yes/No</td> 116<td>N</td> 117</tr> 118 119<tr bgcolor="#FFFFCC"> 120<td> -snucleotide1<br>-snucleotide_seqall</td> 121<td>boolean</td> 122<td>Sequence is nucleotide</td> 123<td>Boolean value Yes/No</td> 124<td>N</td> 125</tr> 126 127<tr bgcolor="#FFFFCC"> 128<td> -sprotein1<br>-sprotein_seqall</td> 129<td>boolean</td> 130<td>Sequence is protein</td> 131<td>Boolean value Yes/No</td> 132<td>N</td> 133</tr> 134 135<tr bgcolor="#FFFFCC"> 136<td> -slower1<br>-slower_seqall</td> 137<td>boolean</td> 138<td>Make lower case</td> 139<td>Boolean value Yes/No</td> 140<td>N</td> 141</tr> 142 143<tr bgcolor="#FFFFCC"> 144<td> -supper1<br>-supper_seqall</td> 145<td>boolean</td> 146<td>Make upper case</td> 147<td>Boolean value Yes/No</td> 148<td>N</td> 149</tr> 150 151<tr bgcolor="#FFFFCC"> 152<td> -scircular1<br>-scircular_seqall</td> 153<td>boolean</td> 154<td>Sequence is circular</td> 155<td>Boolean value Yes/No</td> 156<td>N</td> 157</tr> 158 159<tr bgcolor="#FFFFCC"> 160<td> -squick1<br>-squick_seqall</td> 161<td>boolean</td> 162<td>Read id and sequence only</td> 163<td>Boolean value Yes/No</td> 164<td>N</td> 165</tr> 166 167<tr bgcolor="#FFFFCC"> 168<td> -sformat1<br>-sformat_seqall</td> 169<td>string</td> 170<td>Input sequence format</td> 171<td>Any string</td> 172<td> </td> 173</tr> 174 175<tr bgcolor="#FFFFCC"> 176<td> -iquery1<br>-iquery_seqall</td> 177<td>string</td> 178<td>Input query fields or ID list</td> 179<td>Any string</td> 180<td> </td> 181</tr> 182 183<tr bgcolor="#FFFFCC"> 184<td> -ioffset1<br>-ioffset_seqall</td> 185<td>integer</td> 186<td>Input start position offset</td> 187<td>Any integer value</td> 188<td>0</td> 189</tr> 190 191<tr bgcolor="#FFFFCC"> 192<td> -sdbname1<br>-sdbname_seqall</td> 193<td>string</td> 194<td>Database name</td> 195<td>Any string</td> 196<td> </td> 197</tr> 198 199<tr bgcolor="#FFFFCC"> 200<td> -sid1<br>-sid_seqall</td> 201<td>string</td> 202<td>Entryname</td> 203<td>Any string</td> 204<td> </td> 205</tr> 206 207<tr bgcolor="#FFFFCC"> 208<td> -ufo1<br>-ufo_seqall</td> 209<td>string</td> 210<td>UFO features</td> 211<td>Any string</td> 212<td> </td> 213</tr> 214 215<tr bgcolor="#FFFFCC"> 216<td> -fformat1<br>-fformat_seqall</td> 217<td>string</td> 218<td>Features format</td> 219<td>Any string</td> 220<td> </td> 221</tr> 222 223<tr bgcolor="#FFFFCC"> 224<td> -fopenfile1<br>-fopenfile_seqall</td> 225<td>string</td> 226<td>Features file name</td> 227<td>Any string</td> 228<td> </td> 229</tr> 230 231<tr bgcolor="#FFFFCC"> 232<td align="left" colspan=5>"-outfile" associated outfile qualifiers 233</td> 234</tr> 235 236<tr bgcolor="#FFFFCC"> 237<td> -odirectory2<br>-odirectory_outfile</td> 238<td>string</td> 239<td>Output directory</td> 240<td>Any string</td> 241<td> </td> 242</tr> 243 244<tr bgcolor="#FFFFCC"> 245<td align="left" colspan=5>"-cdsoutseq" associated seqoutall qualifiers 246</td> 247</tr> 248 249<tr bgcolor="#FFFFCC"> 250<td> -osformat3<br>-osformat_cdsoutseq</td> 251<td>string</td> 252<td>Output seq format</td> 253<td>Any string</td> 254<td> </td> 255</tr> 256 257<tr bgcolor="#FFFFCC"> 258<td> -osextension3<br>-osextension_cdsoutseq</td> 259<td>string</td> 260<td>File name extension</td> 261<td>Any string</td> 262<td>cds</td> 263</tr> 264 265<tr bgcolor="#FFFFCC"> 266<td> -osname3<br>-osname_cdsoutseq</td> 267<td>string</td> 268<td>Base file name</td> 269<td>Any string</td> 270<td> </td> 271</tr> 272 273<tr bgcolor="#FFFFCC"> 274<td> -osdirectory3<br>-osdirectory_cdsoutseq</td> 275<td>string</td> 276<td>Output directory</td> 277<td>Any string</td> 278<td> </td> 279</tr> 280 281<tr bgcolor="#FFFFCC"> 282<td> -osdbname3<br>-osdbname_cdsoutseq</td> 283<td>string</td> 284<td>Database name to add</td> 285<td>Any string</td> 286<td> </td> 287</tr> 288 289<tr bgcolor="#FFFFCC"> 290<td> -ossingle3<br>-ossingle_cdsoutseq</td> 291<td>boolean</td> 292<td>Separate file for each entry</td> 293<td>Boolean value Yes/No</td> 294<td>N</td> 295</tr> 296 297<tr bgcolor="#FFFFCC"> 298<td> -oufo3<br>-oufo_cdsoutseq</td> 299<td>string</td> 300<td>UFO features</td> 301<td>Any string</td> 302<td> </td> 303</tr> 304 305<tr bgcolor="#FFFFCC"> 306<td> -offormat3<br>-offormat_cdsoutseq</td> 307<td>string</td> 308<td>Features format</td> 309<td>Any string</td> 310<td> </td> 311</tr> 312 313<tr bgcolor="#FFFFCC"> 314<td> -ofname3<br>-ofname_cdsoutseq</td> 315<td>string</td> 316<td>Features file name</td> 317<td>Any string</td> 318<td> </td> 319</tr> 320 321<tr bgcolor="#FFFFCC"> 322<td> -ofdirectory3<br>-ofdirectory_cdsoutseq</td> 323<td>string</td> 324<td>Output directory</td> 325<td>Any string</td> 326<td> </td> 327</tr> 328 329<tr bgcolor="#FFFFCC"> 330<td align="left" colspan=5>"-mrnaoutseq" associated seqoutall qualifiers 331</td> 332</tr> 333 334<tr bgcolor="#FFFFCC"> 335<td> -osformat4<br>-osformat_mrnaoutseq</td> 336<td>string</td> 337<td>Output seq format</td> 338<td>Any string</td> 339<td> </td> 340</tr> 341 342<tr bgcolor="#FFFFCC"> 343<td> -osextension4<br>-osextension_mrnaoutseq</td> 344<td>string</td> 345<td>File name extension</td> 346<td>Any string</td> 347<td>mrna</td> 348</tr> 349 350<tr bgcolor="#FFFFCC"> 351<td> -osname4<br>-osname_mrnaoutseq</td> 352<td>string</td> 353<td>Base file name</td> 354<td>Any string</td> 355<td> </td> 356</tr> 357 358<tr bgcolor="#FFFFCC"> 359<td> -osdirectory4<br>-osdirectory_mrnaoutseq</td> 360<td>string</td> 361<td>Output directory</td> 362<td>Any string</td> 363<td> </td> 364</tr> 365 366<tr bgcolor="#FFFFCC"> 367<td> -osdbname4<br>-osdbname_mrnaoutseq</td> 368<td>string</td> 369<td>Database name to add</td> 370<td>Any string</td> 371<td> </td> 372</tr> 373 374<tr bgcolor="#FFFFCC"> 375<td> -ossingle4<br>-ossingle_mrnaoutseq</td> 376<td>boolean</td> 377<td>Separate file for each entry</td> 378<td>Boolean value Yes/No</td> 379<td>N</td> 380</tr> 381 382<tr bgcolor="#FFFFCC"> 383<td> -oufo4<br>-oufo_mrnaoutseq</td> 384<td>string</td> 385<td>UFO features</td> 386<td>Any string</td> 387<td> </td> 388</tr> 389 390<tr bgcolor="#FFFFCC"> 391<td> -offormat4<br>-offormat_mrnaoutseq</td> 392<td>string</td> 393<td>Features format</td> 394<td>Any string</td> 395<td> </td> 396</tr> 397 398<tr bgcolor="#FFFFCC"> 399<td> -ofname4<br>-ofname_mrnaoutseq</td> 400<td>string</td> 401<td>Features file name</td> 402<td>Any string</td> 403<td> </td> 404</tr> 405 406<tr bgcolor="#FFFFCC"> 407<td> -ofdirectory4<br>-ofdirectory_mrnaoutseq</td> 408<td>string</td> 409<td>Output directory</td> 410<td>Any string</td> 411<td> </td> 412</tr> 413 414<tr bgcolor="#FFFFCC"> 415<td align="left" colspan=5>"-translationoutseq" associated seqoutall qualifiers 416</td> 417</tr> 418 419<tr bgcolor="#FFFFCC"> 420<td> -osformat5<br>-osformat_translationoutseq</td> 421<td>string</td> 422<td>Output seq format</td> 423<td>Any string</td> 424<td> </td> 425</tr> 426 427<tr bgcolor="#FFFFCC"> 428<td> -osextension5<br>-osextension_translationoutseq</td> 429<td>string</td> 430<td>File name extension</td> 431<td>Any string</td> 432<td>prot</td> 433</tr> 434 435<tr bgcolor="#FFFFCC"> 436<td> -osname5<br>-osname_translationoutseq</td> 437<td>string</td> 438<td>Base file name</td> 439<td>Any string</td> 440<td> </td> 441</tr> 442 443<tr bgcolor="#FFFFCC"> 444<td> -osdirectory5<br>-osdirectory_translationoutseq</td> 445<td>string</td> 446<td>Output directory</td> 447<td>Any string</td> 448<td> </td> 449</tr> 450 451<tr bgcolor="#FFFFCC"> 452<td> -osdbname5<br>-osdbname_translationoutseq</td> 453<td>string</td> 454<td>Database name to add</td> 455<td>Any string</td> 456<td> </td> 457</tr> 458 459<tr bgcolor="#FFFFCC"> 460<td> -ossingle5<br>-ossingle_translationoutseq</td> 461<td>boolean</td> 462<td>Separate file for each entry</td> 463<td>Boolean value Yes/No</td> 464<td>N</td> 465</tr> 466 467<tr bgcolor="#FFFFCC"> 468<td> -oufo5<br>-oufo_translationoutseq</td> 469<td>string</td> 470<td>UFO features</td> 471<td>Any string</td> 472<td> </td> 473</tr> 474 475<tr bgcolor="#FFFFCC"> 476<td> -offormat5<br>-offormat_translationoutseq</td> 477<td>string</td> 478<td>Features format</td> 479<td>Any string</td> 480<td> </td> 481</tr> 482 483<tr bgcolor="#FFFFCC"> 484<td> -ofname5<br>-ofname_translationoutseq</td> 485<td>string</td> 486<td>Features file name</td> 487<td>Any string</td> 488<td> </td> 489</tr> 490 491<tr bgcolor="#FFFFCC"> 492<td> -ofdirectory5<br>-ofdirectory_translationoutseq</td> 493<td>string</td> 494<td>Output directory</td> 495<td>Any string</td> 496<td> </td> 497</tr> 498 499<tr bgcolor="#FFFFCC"> 500<td align="left" colspan=5>"-restoutseq" associated seqoutall qualifiers 501</td> 502</tr> 503 504<tr bgcolor="#FFFFCC"> 505<td> -osformat6<br>-osformat_restoutseq</td> 506<td>string</td> 507<td>Output seq format</td> 508<td>Any string</td> 509<td> </td> 510</tr> 511 512<tr bgcolor="#FFFFCC"> 513<td> -osextension6<br>-osextension_restoutseq</td> 514<td>string</td> 515<td>File name extension</td> 516<td>Any string</td> 517<td>noncoding</td> 518</tr> 519 520<tr bgcolor="#FFFFCC"> 521<td> -osname6<br>-osname_restoutseq</td> 522<td>string</td> 523<td>Base file name</td> 524<td>Any string</td> 525<td> </td> 526</tr> 527 528<tr bgcolor="#FFFFCC"> 529<td> -osdirectory6<br>-osdirectory_restoutseq</td> 530<td>string</td> 531<td>Output directory</td> 532<td>Any string</td> 533<td> </td> 534</tr> 535 536<tr bgcolor="#FFFFCC"> 537<td> -osdbname6<br>-osdbname_restoutseq</td> 538<td>string</td> 539<td>Database name to add</td> 540<td>Any string</td> 541<td> </td> 542</tr> 543 544<tr bgcolor="#FFFFCC"> 545<td> -ossingle6<br>-ossingle_restoutseq</td> 546<td>boolean</td> 547<td>Separate file for each entry</td> 548<td>Boolean value Yes/No</td> 549<td>N</td> 550</tr> 551 552<tr bgcolor="#FFFFCC"> 553<td> -oufo6<br>-oufo_restoutseq</td> 554<td>string</td> 555<td>UFO features</td> 556<td>Any string</td> 557<td> </td> 558</tr> 559 560<tr bgcolor="#FFFFCC"> 561<td> -offormat6<br>-offormat_restoutseq</td> 562<td>string</td> 563<td>Features format</td> 564<td>Any string</td> 565<td> </td> 566</tr> 567 568<tr bgcolor="#FFFFCC"> 569<td> -ofname6<br>-ofname_restoutseq</td> 570<td>string</td> 571<td>Features file name</td> 572<td>Any string</td> 573<td> </td> 574</tr> 575 576<tr bgcolor="#FFFFCC"> 577<td> -ofdirectory6<br>-ofdirectory_restoutseq</td> 578<td>string</td> 579<td>Output directory</td> 580<td>Any string</td> 581<td> </td> 582</tr> 583 584<tr bgcolor="#FFFFCC"> 585<th align="left" colspan=5>General qualifiers</th> 586</tr> 587 588<tr bgcolor="#FFFFCC"> 589<td> -auto</td> 590<td>boolean</td> 591<td>Turn off prompts</td> 592<td>Boolean value Yes/No</td> 593<td>N</td> 594</tr> 595 596<tr bgcolor="#FFFFCC"> 597<td> -stdout</td> 598<td>boolean</td> 599<td>Write first file to standard output</td> 600<td>Boolean value Yes/No</td> 601<td>N</td> 602</tr> 603 604<tr bgcolor="#FFFFCC"> 605<td> -filter</td> 606<td>boolean</td> 607<td>Read first file from standard input, write first file to standard output</td> 608<td>Boolean value Yes/No</td> 609<td>N</td> 610</tr> 611 612<tr bgcolor="#FFFFCC"> 613<td> -options</td> 614<td>boolean</td> 615<td>Prompt for standard and additional values</td> 616<td>Boolean value Yes/No</td> 617<td>N</td> 618</tr> 619 620<tr bgcolor="#FFFFCC"> 621<td> -debug</td> 622<td>boolean</td> 623<td>Write debug output to program.dbg</td> 624<td>Boolean value Yes/No</td> 625<td>N</td> 626</tr> 627 628<tr bgcolor="#FFFFCC"> 629<td> -verbose</td> 630<td>boolean</td> 631<td>Report some/full command line options</td> 632<td>Boolean value Yes/No</td> 633<td>Y</td> 634</tr> 635 636<tr bgcolor="#FFFFCC"> 637<td> -help</td> 638<td>boolean</td> 639<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td> 640<td>Boolean value Yes/No</td> 641<td>N</td> 642</tr> 643 644<tr bgcolor="#FFFFCC"> 645<td> -warning</td> 646<td>boolean</td> 647<td>Report warnings</td> 648<td>Boolean value Yes/No</td> 649<td>Y</td> 650</tr> 651 652<tr bgcolor="#FFFFCC"> 653<td> -error</td> 654<td>boolean</td> 655<td>Report errors</td> 656<td>Boolean value Yes/No</td> 657<td>Y</td> 658</tr> 659 660<tr bgcolor="#FFFFCC"> 661<td> -fatal</td> 662<td>boolean</td> 663<td>Report fatal errors</td> 664<td>Boolean value Yes/No</td> 665<td>Y</td> 666</tr> 667 668<tr bgcolor="#FFFFCC"> 669<td> -die</td> 670<td>boolean</td> 671<td>Report dying program messages</td> 672<td>Boolean value Yes/No</td> 673<td>Y</td> 674</tr> 675 676<tr bgcolor="#FFFFCC"> 677<td> -version</td> 678<td>boolean</td> 679<td>Report version number and exit</td> 680<td>Boolean value Yes/No</td> 681<td>N</td> 682</tr> 683 684</table> 685