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
|
dotpath
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Draw a non-overlapping wordmatch dotplot of two sequences
Description
dotpath generates a dotplot from two input sequences. The dotplot is an
intuitive graphical representation of the regions of similarity between
two sequences. Sequence "words" of a user-specified length are compared
and all exact word matches between the two sequences are recorded. The
set of the longest possible but non-overlapping matches is identified.
The two sequences are the axes of the rectangular dotplot. Wherever
there is an exact matching word in the two sequences a line is plotted.
Algorithm
dotpath uses the same algorithm as diffseq and dottup for finding a
minimal set of exact matches between two sequences. It finds all
identical words of size -wordsize or greater in the two sequences. It
then reduces the matches found to the minimal set of matches that do
not overlap. This set is rendered as lines in the dotplot.
Usage
Here is a sample session with dotpath
% dotpath tembl:AF129756 tembl:BA000025 -word 20 -graph cps -overlaps
Draw a non-overlapping wordmatch dotplot of two sequences
Created dotpath.ps
Go to the input files for this example
Go to the output files for this example
Command line arguments
Draw a non-overlapping wordmatch dotplot of two 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 [4] Word size (Integer 2 or more)
-graph graph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tek, tekt, none, data, xterm, png, gif, pdf,
svg)
Additional (Optional) qualifiers:
-overlaps boolean [N] Displays the overlapping matches (in
red) as well as the minimal set of
non-overlapping matches
-[no]boxit boolean [Y] Draw a box around dotplot
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
"-graph" associated qualifiers
-gprompt boolean Graph prompting
-gdesc string Graph description
-gtitle string Graph title
-gsubtitle string Graph subtitle
-gxtitle string Graph x axis title
-gytitle string Graph y axis title
-goutfile string Output file for non interactive displays
-gdirectory string Output directory
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
Input file format
Input files for usage example
'tembl:AF129756' is a sequence entry in the example nucleic acid
database 'tembl'
Database entry: tembl:AF129756
ID AF129756; SV 1; linear; genomic DNA; STD; HUM; 184666 BP.
XX
AC AF129756;
XX
DT 12-MAR-1999 (Rel. 59, Created)
DT 14-NOV-2006 (Rel. 89, Last updated, Version 5)
XX
DE Homo sapiens MSH55 gene, partial cds; and CLIC1, DDAH, G6b, G6c, G5b, G6d,
DE G6e, G6f, BAT5, G5b, CSK2B, BAT4, G4, Apo M, BAT3, BAT2, AIF-1, 1C7, LST-1,
DE LTB, TNF, and LTA genes, complete cds.
XX
KW .
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 1-184666
RX DOI; 10.1101/gr.1736803.
RX PUBMED; 14656967.
RA Xie T., Rowen L., Aguado B., Ahearn M.E., Madan A., Qin S., Campbell R.D.,
RA Hood L.;
RT "Analysis of the gene-dense major histocompatibility complex class III
RT region and its comparison to mouse";
RL Genome Res. 13(12):2621-2636(2003).
XX
RN [2]
RP 1-184666
RA Rowen L., Madan A., Qin S., Shaffer T., James R., Ratcliffe A., Abbasi N.,
RA Dickhoff R., Loretz C., Madan A., Dors M., Young J., Lasky S., Hood L.;
RT "Sequence of the human major histocompatibility complex class III region";
RL Unpublished.
XX
RN [3]
RP 1-184666
RA Rowen L.;
RT ;
RL Submitted (22-FEB-1999) to the INSDC.
RL Department of Molecular Biotechnology, Box 357730 University of Washington,
RL Seattle, WA 98195, USA
XX
RN [4]
RP 1-184666
RA Rowen L.;
RT ;
RL Submitted (28-OCT-1999) to the INSDC.
RL Multimegabase Sequencing Center, University of Washington, PO Box 357730,
RL Seattle, WA 98195, USA
[Part of this file has been deleted for brevity]
aaaccagttt accaccactc ctaacactaa acttaaatct gactctaaat gtaagtccaa 181740
tctgagccac aagcctaaag ttgaacttta tcctgcttta tgaattattc atccattcct 181800
ccatttagtg agtatctgcg tgcctaacac atgctgggca ttgtcctaag gcaggaggga 181860
catggaggca aagggatcag agaaggtacc agcacctgtg gagcttgtat tccagtgagg 181920
ccagacggaa aagaaagaaa ctgaagaaga aattggtact atgagaaaat aagacaggct 181980
gatgttgtaa gagtggcagg gagctacttt taaatacagt agtcagcaaa atcctctttg 182040
agtgtttggg tggcactgga gctgagaccc aaatgacaaa aaatagtgac caggtaaaag 182100
tttgggagca aagcatttca ggtaaaggga gcagctactg caaaggctgg aaggcggaac 182160
caagctgggg gtgttgacga caaacagaag gccagtgtgg ctggagcaga gagagagact 182220
gggaggcggg tgggagatga ggtcagagag gagggcaggg gccaggtcat gcagggccat 182280
gcaagaaggg taaagcctct agatttcatc cagccacagg aagcctttaa aggtcgtcag 182340
agtgtgtggt gcgtgcgtgt gtgtgtgtgt gtgtgtgtgt gttgcagggg agagaggggg 182400
agggagagag agagagagag agagaagagg gaggtgagca gaggtgattg gatttttttt 182460
tcttttgaca tggtgtcttg ctctgtggcc taggctggag tgcagtggca ccatcatagc 182520
ccactgcaac ctcaaaacca tgggctcaag tcatccttcc acctcagctt cccaagtatc 182580
taggactaca ggtgtgtgcc actgtgcctg gctaatttta aaaaatattt taaaattttt 182640
gttgagacag ggtctatgct gctcaggctg gtctcgaact cctggtttca agtgatctgc 182700
ccatcttggc ctcccaaagt ttttttttgt tagtttgaga ggcggtttcg ctcgttgccc 182760
aggctggagt gcaatgactg atctcatctc actgcaacct ctgcctcctg ggttcaagcg 182820
attctcctgc ttcagcctcc caagtagctg ggattacagg tgcatgccac cattcccggc 182880
taattttttg tatttagtag agatggggtt tcaccatgtt agtcaggctg atctcaaact 182940
cctgacctca ggtgatccgc ctgcctcagc ctcccaaagt tttgggatta caggtgtgag 183000
ccaccatgct gggccagcct cccaaagttt tgggattaca ggcatgagtc accacactgg 183060
ccctggattt tttttctttc ttttttttgg agacggagtc tcactctgtt gcccaggctg 183120
gagtgcaatg gcgtaatctc agctcactgc aacctctgct gcccgggttc aaacgattct 183180
cctgtcttag cctcctgagt agctgggatt ataggtgcat gccaccatgc ctggctaatt 183240
tttgtacttt tagtagagaa agtacaccat cttggccagg ctggtctcga actcctgacc 183300
tcaggtgatc cacttgcgtc ggcctcccaa agtgctggga ttacaggcgt gagacaccgc 183360
acccagcctt tttttttttt tttcttttaa gacagaatcg ctctgtcacc caggctggag 183420
tgcagtggca caatctcggc tcactgcaac ctctgcctcc caggtttaag caatccacct 183480
atgtcagtct cccaagtagc tgggattata ggtgcatgtc accatgcctg gctaattttt 183540
gtacttttag tatagaaagt acaccatgtt ggccaggctg gtcttgaact cctgacctca 183600
agtgatccgc ctgcctcagc ctcccgaagt gctggaatta cagacatgtg ccactgcacc 183660
cggcctggtt ttttttttct aagagatgga gtctcacttt tctgcccagg ttggagtgca 183720
atggcaccat catagctcac tgcagccttc aactcttggc ctcaggcaat ccttgcacct 183780
tagcctcgca gtgttgggat tacaggcatg agccactgag ccttgcctgg actttttttt 183840
ttttttgaga tggcgtctcg ctctgttgcc caggttggag tgctacggca tgatcttggc 183900
tcactgcaac ttccacctcc caggttcaag cgattctctt gcctcggccc cccgagtagc 183960
tgggattaca ggcatgcgcc accgtgcctg gctaattttg gtatttttag tagagatagg 184020
gtttcatcat gttgggcagg ctggtcttga actcctgacc tcgtgatcca cccacctcgg 184080
cctcccaaag tgctgggatt ataggcatag ccaacgcgcc cagcctggac ttgtttttaa 184140
aagatcactg tggctcctgt gtttaggctg gctggtagga gacaggtggc agtggcattg 184200
atggtgaaga gaaaatagtg gcagccatgg agatggagag aagtagacaa gtttgggata 184260
tattatacat tccaggggta gaaacaacag gactagatga tggattgatg ggtgggagat 184320
gtagatactg ggagagaagc aggattctga tggatggaaa aactaaaaaa ttctattttg 184380
ggtgtggtaa gtctaagtct attagacatg caagtagaga tgtcactggg cagatacaca 184440
tctggatttc aggggcaagg tccaagctag agaaagaaac ctgggcatgg tcagcatgag 184500
gatggtgttt aaagccatgg aacttatctt gtgcatccct ataagacccc tttgaggcac 184560
ttgtttcccc tcacaatgga tgcagtgcat cttccattct gaattccaga ggcaacaacc 184620
tcctgctcct agaagctaaa ctctccagac ttagtcttct gaattc 184666
//
Database entry: tembl:BA000025
ID BA000025; SV 2; linear; genomic DNA; STD; HUM; 2229817 BP.
XX
AC BA000025; AP000502-AP000521;
XX
DT 09-DEC-2004 (Rel. 82, Created)
DT 17-JUN-2008 (Rel. 96, Last updated, Version 5)
XX
DE Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region.
XX
KW .
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 1-2229817
RA Hirakawa M., Yamaguchi H., Imai K., Shimada J.;
RT ;
RL Submitted (21-AUG-2001) to the INSDC.
RL Mika Hirakawa, Japan Science and Technology Corporation (JST), Advanced
RL Databases Department; 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan
RL (E-mail:mika@tokyo.jst.go.jp, URL:http://www-alis.tokyo.jst.go.jp/,
RL Tel:81-3-5214-8491, Fax:81-3-5214-8470)
XX
RN [2]
RA Shiina S., Tamiya G., Oka A., Inoko H.;
RT "Homo sapiens 2,229,817bp genomic DNA of 6p21.3 HLA class I region";
RL Unpublished.
XX
DR EPD; EP11158; HS_TNF.
DR EPD; EP11159; HS_LTA.
DR EPD; EP73522; HS_HLA-B.
DR EPD; EP73908; HS_GTF2H4.
DR EPD; EP73940; HS_NEU1.
DR EPD; EP74013; HS_VARS2.
DR EPD; EP74203; HS_MRPS18B.
DR EPD; EP74346; HS_HLA-E.
DR EPD; EP74389; HS_BAT1.
DR EPD; EP74485; HS_IER3.
DR Ensembl-Gn; ENSG00000096155; Homo_sapiens.
DR Ensembl-Gn; ENSG00000096171; Homo_sapiens.
DR Ensembl-Gn; ENSG00000111971; Homo_sapiens.
DR Ensembl-Gn; ENSG00000137310; Homo_sapiens.
DR Ensembl-Gn; ENSG00000137312; Homo_sapiens.
DR Ensembl-Gn; ENSG00000137313; Homo_sapiens.
DR Ensembl-Gn; ENSG00000137331; Homo_sapiens.
DR Ensembl-Gn; ENSG00000137332; Homo_sapiens.
DR Ensembl-Gn; ENSG00000137337; Homo_sapiens.
[Part of this file has been deleted for brevity]
ttggccccac cccagcatgt ctccaggttc ctctcagccc tggttccttt tggccctgca 2226900
gtcacaatgg gcaacactgt gacgcaccct gtcctgtgtc acagtgtcat acactcaggc 2226960
tcacattgcc cctaggccac ttgccagcca agggacatgg ccacattttg tgtcttctgc 2227020
acctcagcct tgctttcaag tgcaggtgat gatggcaccc acgcagaaca aatgttattt 2227080
gctatcttcg tcgagtttag tcatccaatt ttccaaccct cactgggcaa ggaagagtgt 2227140
ggtttccacc aagaaggcag gatgtcagca gtcacagggg caaccaacag ggaaagccgc 2227200
cggaaaatag accccacagg aagcacaggt gtccagtgga gatgggaacc ctgcagattt 2227260
gaccgtcttt aagcagatta gagagattac cgttactaac aacttagcca taaaagttta 2227320
ttagctattt tcaaaaagca taaaattatg taatataatt ttttttaaat ttccatcaat 2227380
acaaaactaa tctgggcact gcaacttccg gtgggcaact gggataggcg gcatcatcag 2227440
gaaggcgagc cctgccgtgc cccatgtgcc agtgccccag atggcggcag cctccccaga 2227500
agcaccttgt atctcccctg cacagggcca gggtcccagc ttcccataca ccttctcctg 2227560
ctttttcttt tctgtccttt cctttttcaa taaaccacct gcaaaaaggg aaaaccattc 2227620
tgaggacaag aaacatgtca atgggaaata cacagttgcc agagggtaaa aggccctgtt 2227680
cattctcatt gaaaagctca ggtatttctg ttaaagtctc tccttttact ttaggatgct 2227740
gactcctgcg tccatctcaa cctgggcatc gtgccaccac cttcaagaag agaaaaacta 2227800
agtagtgctt tgcaaagggg cagcagcatt tctcatttct gaccatgtca ggcacatggc 2227860
catgcagatg agcaggtggg ggacacaggt gagtctccag acctgctctc ctcccacagt 2227920
acattcttga gtctttttaa acagttgtga aaatgccaca gatgcaagca cctgtgggcc 2227980
actcccatgg ggaccgttgc acaaggcagt gccactcatt ctcagaacct cctaccatgg 2228040
gctatgctta gtgacccgag gccaagccaa ggaagacgcc agccacaggg tgccatcctc 2228100
aggggcatgc tgccagcagg ggcaaagtta tccctagcaa caagatacag aaagaaagaa 2228160
aaaaggaagg aaatgtagcc aatgggccgg ttcaggttct tgactttgcc acacaaaaga 2228220
atttgagagc aagtccaaag taaaagtcag caagagaatt tattgcaaag tgaaagtaca 2228280
ctctgacagc tgatcagagc agctgctcaa aagagagaca gtaccctccc ctcacgggag 2228340
tcttacatga ttattcatga ataggtggga aggggtattg ttttaagcat gttctgtggt 2228400
ctcttgaacg tgcatgcact gtggttgtac atatcagcac acacatctta cgtctcatta 2228460
gcatcttaac ttccctctca gagttgtgtt tgctactatt gtaatgagca taggtcagcc 2228520
caaggacact attcatgggt ttctgggctt cctcagatgt ggggatgcct cccttggctc 2228580
ttctacctct ttgctgcagg atgttctaac cacaagccca ggatatggtt tgcgcactgt 2228640
cgaacagctt gttctctcca tcaacctgac aagtctcttg tttcctttca agggaggctg 2228700
tgaacaccct atctcactga cctcagaagg acagtacagc agtagccacc atgaccaaaa 2228760
agatgattcc agaagtgcag gacaactccc tacccagagg ctgtggctgt gcagtaacac 2228820
accaagaggg gagtccagct ggctctcagg gtgctcacta ccctcatctg ggggcctgga 2228880
ggacgtcaat tcctgagaac gccacgttct agtgagtaga atgaactgag agatacacag 2228940
caaagctcca catacttttc cttttctttg tgcccgcagt gttcttcatc agtgtgctct 2229000
cgcttttcag ctactactgt tggctggctg gaaaaaatag aacaatagta aaaattagag 2229060
accagtcttt ggtgatgaag agaaatattg gctacttcca gtattttcta gctttggtta 2229120
tggttgcagt tttccagctc accttgtggg gatgaattca gaaaaaagtt acaaattgaa 2229180
atgaacatgc cagaagtatt ggctcaaatc aacgttgtcc tattaagcca cttagtgaat 2229240
caaaagaccg cttgttggac tgttaatctc ggtggccaga gaaaggagct gaagaaggtg 2229300
ttgccagatc aggaacaaat aattacagcg gcaatagaaa atggaagacc acttgttcat 2229360
aaccatttga ataagggcaa ggtgtatgga aacacattat gaactgatat tttcagtttt 2229420
gtttgcaaga aaatgattaa taaggtgaaa taattgaagt atcacggaag atacattaaa 2229480
aaaaaaaaaa gcctttgtac agtttgctgg agccacagat gtcctactcc agagcagaac 2229540
aatgcctgaa tcttcagggt ccatttctgc cgcattcact agcaaccaca aatgtgactt 2229600
aattttactt tggaaataat gcttacccat tgtgagatgc tgtaatatga accatcatta 2229660
catgttaaca tggcacatgg aattttgagt gtctaagtta catttttaga gttgtttctt 2229720
agtagccatg tgagtttcca ctccaaaaac acaagctaaa aacttgtttt gagtgaagga 2229780
catctagggc aaatggtggc tgaaagtgaa tgagatc 2229817
//
Output file format
In normal operation, a dotplot image is displayed.
With the -data qualifier a file of the positions of the matches in the
minimal non-overlapping set of matches is output.
Output files for usage example
Graphics File: dotpath.ps
[dotpath results]
Notes
For similar sequences, dotpath provides a convenient way to find a path
that aligns the two sequences well. It is not a true optimal path as
produced by the dynamic programming algorithms used in water or needle,
but for very closely related sequences it will produce the same result.
In contast to full alignment, it works very quickly with very long
sequences.
The entire set of matches found can be displayed with the -overlaps
qualifier. This shows all matches in red, except for those in the
minimal path (non-overlapping set) which are shown in black, as normal.
Using a longer word size will create a dottplot with relatively less
noise; the matches are longer and therefore more likely to have
biological meaning. Such runs will be much faster, but of course are
less sensitive.
References
None
Warnings
If you give a small word size with a very large sequence you will run
out of memory. If this happens, try again with a larger word size.
Diagnostic Error Messages
None
Exit status
It always exits with status 0.
Known bugs
None
See also
Program name Description
dotmatcher Draw a threshold dotplot of two sequences
dottup Display a wordmatch dotplot of two sequences
polydot Draw dotplots for all-against-all comparison of a sequence set
This program is closely based on dottup with the addition of by default
displaying only the minimal set of non-overlapping matches.
This program uses the same algorithm as diffseq for finding a minimal
set of very good matches between two sequences. diffseq may be more
convenient if you are looking at the differences between two nearly
identical sequences.
Author(s)
Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
History
Written 14 Aug 2000.
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
|
