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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408
|
<HTML>
<HEAD>
<TITLE>
EMBOSS
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
diffseq
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Wiki
</H2>
The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.
<p>
Please help by correcting and extending the Wiki pages.
<H2>
Function
</H2>
Compare and report features of two similar sequences
<H2>
Description
</H2>
<p><b>diffseq</b> reads two sequences which typically are very similar
or almost identical. It finds regions of overlap between the two
sequences and reports on differences between the features of the two
sequences within these regions. The output is a standard EMBOSS
report file. The start and end positions of the regions of overlap
are reported. Any differences between the sequences, and any features
(except the source feature) that overlap those differences, are
included in the output report.</p>
<p>The differences are also reported for each input sequence as two
separate feature table output files.</p>
<H2>
Algorithm
</H2>
<p><b>diffseq</b> searches for identical matches between all sequence
words from both sequences. Identical sequence regions are found by
creating a hash table of subsequences of user-defined size (-wordsize
option), which is 10 by default. It then reduces the matches to a
minimum set of overlapping matches by sorting them in order of size
(largest size first). For each such match it removes any smaller
matches that overlap. The result is a set of the longest regions of
identity between the two sequences that do not overlap with each
other. The mismatched regions between these matches are reported.</p>
<H2>
Usage
</H2>
Here is a sample session with <b>diffseq</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>diffseq tembl:x65923 tembl:ay411291 </b>
Compare and report features of two similar sequences
Word size [10]: <b></b>
Output report [x65923.diffseq]: <b></b>
Features output [X65923.diffgff]: <b></b>
Second features output [AY411291.diffgff]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Compare and report features of two similar sequences
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-asequence] sequence Sequence filename and optional format, or
reference (input USA)
[-bsequence] sequence Sequence filename and optional format, or
reference (input USA)
-wordsize integer [10] The similar regions between the two
sequences are found by creating a hash table
of 'wordsize'd subsequences. 10 is a
reasonable default. Making this value larger
(20?) may speed up the program slightly,
but will mean that any two differences
within 'wordsize' of each other will be
grouped as a single region of difference.
This value may be made smaller (4?) to
improve the resolution of nearby
differences, but the program will go much
slower. (Integer 2 or more)
[-outfile] report [*.diffseq] Output report file name (default
-rformat diffseq)
[-aoutfeat] featout [$(asequence.name).diffgff] File for output
of first sequence's features
[-boutfeat] featout [$(bsequence.name).diffgff] File for output
of second sequence's features
Additional (Optional) qualifiers:
-globaldifferences boolean [N] Normally this program will find regions
of identity that are the length of the
specified word-size or greater and will then
report the regions of difference between
these matching regions. This works well and
is what most people want if they are working
with long overlapping nucleic acid
sequences. You are usually not interested in
the non-overlapping ends of these
sequences. If you have protein sequences or
short RNA sequences however, you will be
interested in differences at the very ends .
It this option is set to be true then the
differences at the ends will also be
reported.
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-asequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-bsequence" associated qualifiers
-sbegin2 integer Start of the sequence to be used
-send2 integer End of the sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-scircular2 boolean Sequence is circular
-squick2 boolean Read id and sequence only
-sformat2 string Input sequence format
-iquery2 string Input query fields or ID list
-ioffset2 integer Input start position offset
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
"-outfile" associated qualifiers
-rformat3 string Report format
-rname3 string Base file name
-rextension3 string File name extension
-rdirectory3 string Output directory
-raccshow3 boolean Show accession number in the report
-rdesshow3 boolean Show description in the report
-rscoreshow3 boolean Show the score in the report
-rstrandshow3 boolean Show the nucleotide strand in the report
-rusashow3 boolean Show the full USA in the report
-rmaxall3 integer Maximum total hits to report
-rmaxseq3 integer Maximum hits to report for one sequence
"-aoutfeat" associated qualifiers
-offormat4 string Output feature format
-ofopenfile4 string Features file name
-ofextension4 string File name extension
-ofdirectory4 string Output directory
-ofname4 string Base file name
-ofsingle4 boolean Separate file for each entry
"-boutfeat" associated qualifiers
-offormat5 string Output feature format
-ofopenfile5 string Features file name
-ofextension5 string File name extension
-ofdirectory5 string Output directory
-ofname5 string Base file name
-ofsingle5 boolean Separate file for each entry
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>
<tr bgcolor="#FFFFCC">
<td>[-asequence]<br>(Parameter 1)</td>
<td>sequence</td>
<td>Sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>
<tr bgcolor="#FFFFCC">
<td>[-bsequence]<br>(Parameter 2)</td>
<td>sequence</td>
<td>Sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-wordsize</td>
<td>integer</td>
<td>The similar regions between the two sequences are found by creating a hash table of 'wordsize'd subsequences. 10 is a reasonable default. Making this value larger (20?) may speed up the program slightly, but will mean that any two differences within 'wordsize' of each other will be grouped as a single region of difference. This value may be made smaller (4?) to improve the resolution of nearby differences, but the program will go much slower.</td>
<td>Integer 2 or more</td>
<td>10</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 3)</td>
<td>report</td>
<td>Output report file name</td>
<td>(default -rformat diffseq)</td>
<td><i><*></i>.diffseq</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>[-aoutfeat]<br>(Parameter 4)</td>
<td>featout</td>
<td>File for output of first sequence's features</td>
<td>Writeable feature table</td>
<td>$(asequence.name).diffgff</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>[-boutfeat]<br>(Parameter 5)</td>
<td>featout</td>
<td>File for output of second sequence's features</td>
<td>Writeable feature table</td>
<td>$(bsequence.name).diffgff</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>
<tr bgcolor="#FFFFCC">
<td>-globaldifferences</td>
<td>boolean</td>
<td>Normally this program will find regions of identity that are the length of the specified word-size or greater and will then report the regions of difference between these matching regions. This works well and is what most people want if they are working with long overlapping nucleic acid sequences. You are usually not interested in the non-overlapping ends of these sequences. If you have protein sequences or short RNA sequences however, you will be interested in differences at the very ends . It this option is set to be true then the differences at the ends will also be reported.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>
<tr>
<td colspan=5>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>
<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-asequence" associated sequence qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sbegin1<br>-sbegin_asequence</td>
<td>integer</td>
<td>Start of the sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -send1<br>-send_asequence</td>
<td>integer</td>
<td>End of the sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sreverse1<br>-sreverse_asequence</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sask1<br>-sask_asequence</td>
<td>boolean</td>
<td>Ask for begin/end/reverse</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -snucleotide1<br>-snucleotide_asequence</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sprotein1<br>-sprotein_asequence</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -slower1<br>-slower_asequence</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -supper1<br>-supper_asequence</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -scircular1<br>-scircular_asequence</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -squick1<br>-squick_asequence</td>
<td>boolean</td>
<td>Read id and sequence only</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sformat1<br>-sformat_asequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_asequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ioffset1<br>-ioffset_asequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sdbname1<br>-sdbname_asequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sid1<br>-sid_asequence</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ufo1<br>-ufo_asequence</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -fformat1<br>-fformat_asequence</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -fopenfile1<br>-fopenfile_asequence</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-bsequence" associated sequence qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sbegin2<br>-sbegin_bsequence</td>
<td>integer</td>
<td>Start of the sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -send2<br>-send_bsequence</td>
<td>integer</td>
<td>End of the sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sreverse2<br>-sreverse_bsequence</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sask2<br>-sask_bsequence</td>
<td>boolean</td>
<td>Ask for begin/end/reverse</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -snucleotide2<br>-snucleotide_bsequence</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sprotein2<br>-sprotein_bsequence</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -slower2<br>-slower_bsequence</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -supper2<br>-supper_bsequence</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -scircular2<br>-scircular_bsequence</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -squick2<br>-squick_bsequence</td>
<td>boolean</td>
<td>Read id and sequence only</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sformat2<br>-sformat_bsequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -iquery2<br>-iquery_bsequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ioffset2<br>-ioffset_bsequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sdbname2<br>-sdbname_bsequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -sid2<br>-sid_bsequence</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ufo2<br>-ufo_bsequence</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -fformat2<br>-fformat_bsequence</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -fopenfile2<br>-fopenfile_bsequence</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated report qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -rformat3<br>-rformat_outfile</td>
<td>string</td>
<td>Report format</td>
<td>Any string</td>
<td>diffseq</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -rname3<br>-rname_outfile</td>
<td>string</td>
<td>Base file name</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -rextension3<br>-rextension_outfile</td>
<td>string</td>
<td>File name extension</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -rdirectory3<br>-rdirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -raccshow3<br>-raccshow_outfile</td>
<td>boolean</td>
<td>Show accession number in the report</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -rdesshow3<br>-rdesshow_outfile</td>
<td>boolean</td>
<td>Show description in the report</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -rscoreshow3<br>-rscoreshow_outfile</td>
<td>boolean</td>
<td>Show the score in the report</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -rstrandshow3<br>-rstrandshow_outfile</td>
<td>boolean</td>
<td>Show the nucleotide strand in the report</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -rusashow3<br>-rusashow_outfile</td>
<td>boolean</td>
<td>Show the full USA in the report</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -rmaxall3<br>-rmaxall_outfile</td>
<td>integer</td>
<td>Maximum total hits to report</td>
<td>Any integer value</td>
<td>0</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -rmaxseq3<br>-rmaxseq_outfile</td>
<td>integer</td>
<td>Maximum hits to report for one sequence</td>
<td>Any integer value</td>
<td>0</td>
</tr>
<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-aoutfeat" associated featout qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -offormat4<br>-offormat_aoutfeat</td>
<td>string</td>
<td>Output feature format</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ofopenfile4<br>-ofopenfile_aoutfeat</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ofextension4<br>-ofextension_aoutfeat</td>
<td>string</td>
<td>File name extension</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ofdirectory4<br>-ofdirectory_aoutfeat</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ofname4<br>-ofname_aoutfeat</td>
<td>string</td>
<td>Base file name</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ofsingle4<br>-ofsingle_aoutfeat</td>
<td>boolean</td>
<td>Separate file for each entry</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-boutfeat" associated featout qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -offormat5<br>-offormat_boutfeat</td>
<td>string</td>
<td>Output feature format</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ofopenfile5<br>-ofopenfile_boutfeat</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ofextension5<br>-ofextension_boutfeat</td>
<td>string</td>
<td>File name extension</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ofdirectory5<br>-ofdirectory_boutfeat</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ofname5<br>-ofname_boutfeat</td>
<td>string</td>
<td>Base file name</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -ofsingle5<br>-ofsingle_boutfeat</td>
<td>boolean</td>
<td>Separate file for each entry</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>
<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
</table>
<H2>
Input file format
</H2>
This program reads in two nucleotide or protein sequences
<p>
<p>
The input is a standard EMBOSS sequence query (also known as a 'USA').
<p>
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl
<p>
Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.
<p>
The input format can be specified by using the
command-line qualifier <tt>-sformat xxx</tt>, where 'xxx' is replaced
by the name of the required format. The available format names are:
gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
(nbrf), swissprot (swiss, sw), dasgff and debug.
<p>
See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:x65923' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:x65923</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC X65923;
XX
DT 13-MAY-1992 (Rel. 31, Created)
DT 18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE H.sapiens fau mRNA
XX
KW fau gene.
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
XX
RN [1]
RP 1-518
RA Michiels L.M.R.;
RT ;
RL Submitted (29-APR-1992) to the INSDC.
RL L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN [2]
RP 1-518
RX PUBMED; 8395683.
RA Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8(9):2537-2546(1993).
XX
DR Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR Ensembl-Tr; ENST00000531743; Homo_sapiens.
XX
FH Key Location/Qualifiers
FH
FT source 1..518
FT /organism="Homo sapiens"
FT /chromosome="11q"
FT /map="13"
FT /mol_type="mRNA"
FT /clone_lib="cDNA"
FT /clone="pUIA 631"
FT /tissue_type="placenta"
FT /db_xref="taxon:9606"
FT misc_feature 57..278
FT /note="ubiquitin like part"
FT CDS 57..458
FT /gene="fau"
FT /db_xref="GDB:135476"
FT /db_xref="GOA:P35544"
FT /db_xref="GOA:P62861"
FT /db_xref="H-InvDB:HIT000322806.14"
FT /db_xref="HGNC:3597"
FT /db_xref="InterPro:IPR000626"
FT /db_xref="InterPro:IPR006846"
FT /db_xref="InterPro:IPR019954"
FT /db_xref="InterPro:IPR019955"
FT /db_xref="InterPro:IPR019956"
FT /db_xref="PDB:2L7R"
FT /db_xref="UniProtKB/Swiss-Prot:P35544"
FT /db_xref="UniProtKB/Swiss-Prot:P62861"
FT /protein_id="CAA46716.1"
FT /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT misc_feature 98..102
FT /note="nucleolar localization signal"
FT misc_feature 279..458
FT /note="S30 part"
FT polyA_signal 484..489
FT polyA_site 509
XX
SQ Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc 60
agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg 120
cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc 180
tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc 240
tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 300
gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga 360
agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca 420
cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc 480
tctaataaaa aagccactta gttcagtcaa aaaaaaaa 518
//
</pre>
</td></tr></table><p>
<p><h3>Database entry: tembl:ay411291</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID AY411291; SV 1; linear; genomic DNA; GSS; HUM; 402 BP.
XX
AC AY411291;
XX
DT 13-DEC-2003 (Rel. 78, Created)
DT 17-DEC-2003 (Rel. 78, Last updated, Version 2)
XX
DE Homo sapiens FAU gene, VIRTUAL TRANSCRIPT, partial sequence, genomic survey
DE sequence.
XX
KW GSS.
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
XX
RN [1]
RP 1-402
RX DOI; 10.1126/science.1088821.
RX PUBMED; 14671302.
RA Clark A.G., Glanowski S., Nielson R., Thomas P., Kejariwal A., Todd M.A.,
RA Tanenbaum D.M., Civello D.R., Lu F., Murphy B., Ferriera S., Wang G.,
RA Zheng X.H., White T.J., Sninsky J.J., Adams M.D., Cargill M.;
RT "Inferring nonneutral evolution from human-chimp-mouse orthologous gene
RT trios";
RL Science 302(5652):1960-1963(2003).
XX
RN [2]
RP 1-402
RA Clark A.G., Glanowski S., Nielson R., Thomas P., Kejariwal A., Todd M.A.,
RA Tanenbaum D.M., Civello D.R., Lu F., Murphy B., Ferriera S., Wang G.,
RA Zheng X.H., White T.J., Sninsky J.J., Adams M.D., Cargill M.;
RT ;
RL Submitted (16-NOV-2003) to the INSDC.
RL Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
XX
CC This sequence was made by sequencing genomic exons and ordering
CC them based on alignment.
XX
FH Key Location/Qualifiers
FH
FT source 1..402
FT /organism="Homo sapiens"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:9606"
FT gene <1..>402
FT /gene="FAU"
FT /locus_tag="HCM4175"
XX
SQ Sequence 402 BP; 95 A; 110 C; 129 G; 68 T; 0 other;
atgcagctct ttgtccgcgc ccaggagcta cacaccttcg aggtgaccgg ccaggaaacg 60
gtcgcccaga tcaaggctca tgtagcctca ctggagggca ttgccccgga agatcaagtc 120
gtgctcctgg caggcgcgcc cctggaggat gaggccactc tgggccagtg cggggtggag 180
gccctgacta ccctggaagt agcaggccgc atgcttggag gtaaagtcca tggttccctg 240
gcccgtgctg gaaaagtgag aggtcagact cctaaggtgg ccaaacagga gaagaagaag 300
aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt caacgttgtg 360
cccacctttg gcaagaagaa gggccccaat gccaactctt aa 402
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<p>
The output is a standard EMBOSS report file.
<p>
The results can be output in one of several styles by using the
command-line qualifier <tt>-rformat xxx</tt>, where 'xxx' is replaced
by the name of the required format. The available format names are:
embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif,
diffseq, draw, restrict, excel, feattable, motif, nametable, regions,
seqtable, simple, srs, table, tagseq.
<p>
See:
<A href="http://emboss.sf.net/docs/themes/ReportFormats.html">
http://emboss.sf.net/docs/themes/ReportFormats.html</A>
for further information on report formats.
<p>
<p>
By default <b>diffseq</b> writes a 'diffseq' report file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: x65923.diffseq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: diffseq
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: diffseq
# [-asequence] tembl:x65923
# [-bsequence] tembl:ay411291
# Report_format: diffseq
# Report_file: x65923.diffseq
# Additional_files: 2
# 1: X65923.diffgff (Feature file for first sequence)
# 2: AY411291.diffgff (Feature file for second sequence)
########################################
#=======================================
#
# Sequence: X65923 from: 1 to: 518
# HitCount: 1
#
# Compare: AY411291 from: 1 to: 402
#
# X65923 overlap starts at 57
# AY411291 overlap starts at 1
#
#
#=======================================
X65923 284-284 Length: 1
Feature: CDS 57-458 gene='fau' db_xref='GDB:135476' db_xref='GOA:P35544' db_xref='GOA:P62861' db_xref='H-InvDB:HIT000322806.14' db_xref='HGNC:3597' db_xref='InterPro:IPR000626' db_xref='InterPro:IPR006846' db_xref='InterPro:IPR019954' db_xref='InterPro:IPR019955' db_xref='InterPro:IPR019956' db_xref='PDB:2L7R' db_xref='UniProtKB/Swiss-Prot:P35544' db_xref='UniProtKB/Swiss-Prot:P62861' protein_id='CAA46716.1'
Feature: misc_feature 279-458 note='S30 part'
Sequence: t
Sequence: c
Feature: gene 1-402 gene='FAU' locus_tag='HCM4175'
AY411291 228-228 Length: 1
#---------------------------------------
#
# Overlap_end: 458 in X65923
# Overlap_end: 402 in AY411291
#
# SNP_count: 1
# Transitions: 1
# Transversions: 0
#
#---------------------------------------
#---------------------------------------
# Total_sequences: 2
# Total_length: 920
# Reported_sequences: 1
# Reported_hitcount: 1
#---------------------------------------
</pre>
</td></tr></table><p>
<p><h3>File: AY411291.diffgff</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
##gff-version 3
##sequence-region AY411291 1 402
#!Date 2013-07-15
#!Type DNA
#!Source-version EMBOSS 6.6.0.0
AY411291 diffseq sequence_conflict 228 228 1 + . ID=AY411291.1;note=SNP in X65923;replace=t
</pre>
</td></tr></table><p>
<p><h3>File: X65923.diffgff</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
##gff-version 3
##sequence-region X65923 1 518
#!Date 2013-07-15
#!Type DNA
#!Source-version EMBOSS 6.6.0.0
X65923 diffseq sequence_conflict 284 284 1 + . ID=X65923.1;note=SNP in AY411291;replace=c
</pre>
</td></tr></table><p>
<p>
The first line is the title giving the names of the sequences used.
<p>
The next two non-blank lines state the positions in each sequence
where the detected overlap between them starts.
<p>
There then follows a set of reports of the mismatches between the sequences.
<br>
Each report consists of 4 or more lines.
<br>
<ul>
<li>The first line has the name of the first sequence followed by the
start and end positions of the mismatched region in that sequence,
followed by the length of the mismatched region. If the mismatched
region is of zero length in this sequence, then only the position of
the last matching base before the mismatch is given.</li>
<li>If a feature of the first sequence overlaps with this mismatch
region, then one or more lines starting with 'Feature:' comes next
with the type, position and tag field of the feature.</li>
<li>Next is a line starting "Sequence:" giving the sequence of the
mismatch in the first sequence.</li> </ul>
<p>
This is followed by the equivalent information for the second
sequence, but in the reverse order, namely 'Sequence:' line,
'Feature:' lines and line giving the position of the mismatch in the
second sequence.
<p>
At the end of the report are two non-blank lines giving the positions in each
sequence where the detected
overlap between them ends.
<p>
The last three lines of the report gives the counts of SNPs (defined
as a change of one nucleotide to one other nucleotide, no deletions or
insertions are counted, no multi-base changes are counted).
<p>
If the input sequences are nucleic acid, The counts of transitions
(Pyrimide to Pyrimidine or Purine to Purine) and transversions
(Pyrimidine to Purine) are also given.
<p>
It should be noted that not all features are reported.
<p>
The 'source' feature found in all EMBL/Genbank feature table entries is
not reported as this covers all of the sequence and so overlaps with any
difference found in that sequence and so is uninformative and
irritating. It has therefore been removed from the output report.
<p>
The translation information of CDS features is often extremely long and
does not add useful information to the report. It has therefore been
removed from the output report.
<H2>
Data files
</H2>
None
<H2>
Notes
</H2>
<p><b>diffseq</b> is useful when looking for SNPs, differences between
strains of an organism and anything else that requires the differences
between two eseentially identical sequences to be highlighted.</p>
<p>Identical sequence regions are found by creating a hash table of
subsequences of user-defined size (-wordsize option, which is 10 by
default). Making this value larger (e.g. 20) may speed-up the program
slightly, but will mean that any two differences
within <tt>wordsize</tt> bases bases or residues of each other will be
grouped as a single region of difference. This value may be made
smaller to improve the resolution of nearby differences, but the
program will go much slower.</p>
<p>The sequences can be very long; it should be possible to find
differences between sequences that are Mega-bases long. If, however,
you run out of memory, use a larger word size. This increases the
length between mismatches that will be reported as one event. Thus a
word size of 50 will report two single-base differences that are with
50 bases of each other as one mismatch.</p>
<p>By default, <b>diffseq</b> finds regions of identity that are at
least as long as the specified word-size. This is what is typically
required when working with long overlapping nucleic acid sequences,
where the non-overlapping sequence ends are less interesting. If
however, you have protein sequences or short RNA sequences then
you may well be interested in differences at the very ends.
The <tt>-globaldifferences</tt> option when set means the differences
at the ends will also be reported.</p>
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
</table>
<H2>
Author(s)
</H2>
Gary Williams formerly at:
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
<p>
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
<H2>
History
</H2>
Written 15th Aug 2000 - Gary Williams.
<p>
18th Aug 2000 - Added writing out GFF files of the mismatched regions
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
</BODY>
</HTML>
|