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
|
palindrome
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
Find inverted repeats in nucleotide sequence(s)
Description
palindrome finds inverted repeats (stem loops) in nucleotide sequences.
It will find inverted repeats that include a proportion of mismatches
and gaps, that correspond to bulges in the stem loop. It finds all
possible inverted matches satisfying the specified conditions of
minimum and maximum length of palindrome, maximum gap between repeated
regions and number of mismatches allowed.
Usage
Here is a sample session with palindrome
% palindrome
Find inverted repeats in nucleotide sequence(s)
Input nucleotide sequence(s): tembl:d00596
Enter minimum length of palindrome [10]: 15
Enter maximum length of palindrome [100]:
Enter maximum gap between repeated regions [100]:
Number of mismatches allowed [0]:
Output file [d00596.pal]:
Report overlapping matches [Y]:
Go to the input files for this example
Go to the output files for this example
Command line arguments
Find inverted repeats in nucleotide sequence(s)
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
-minpallen integer [10] Enter minimum length of palindrome
(Integer 1 or more)
-maxpallen integer [100] Enter maximum length of palindrome
(Any integer value)
-gaplimit integer [100] Enter maximum gap between repeated
regions (Integer 0 or more)
-nummismatches integer [0] Number of mismatches allowed (Positive
integer)
[-outfile] outfile [*.palindrome] Output file name
-[no]overlap boolean [Y] Report overlapping matches
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each 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
"-outfile" associated qualifiers
-odirectory2 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
palindrome reads one or more nucleotide sequences.
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier
-sformat xxx, 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.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
information on sequence formats.
Input files for usage example
'tembl:d00596' is a sequence entry in the example nucleic acid database
'tembl'
Database entry: tembl:d00596
ID D00596; SV 1; linear; genomic DNA; STD; HUM; 18596 BP.
XX
AC D00596;
XX
DT 17-JUL-1991 (Rel. 28, Created)
DT 07-DEC-2007 (Rel. 94, Last updated, Version 6)
XX
DE Homo sapiens gene for thymidylate synthase, 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 1-18596
RX PUBMED; 2243092.
RA Kaneda S., Nalbantoglu J., Takeishi K., Shimizu K., Gotoh O., Seno T.,
RA Ayusawa D.;
RT "Structural and functional analysis of the human thymidylate synthase
RT gene";
RL J Biol Chem 265(33):20277-20284(1990).
XX
DR Ensembl-Gn; ENSG00000176890; Homo_sapiens.
DR Ensembl-Tr; ENST00000323274; Homo_sapiens.
DR GDB; 163670.
DR GDB; 182340.
XX
CC These data kindly submitted in computer readable form by:
CC Sumiko Kaneda
CC National Institute of Genetics
CC 1111 Yata
CC Mishima 411
CC Japan
XX
FH Key Location/Qualifiers
FH
FT source 1..18596
FT /organism="Homo sapiens"
FT /chromosome="18"
FT /map="18p11.32"
FT /mol_type="genomic DNA"
FT /clone="lambdaHTS-1 and lambdaHTS-3"
FT /db_xref="taxon:9606"
FT repeat_region 1..148
FT /rpt_family="Alu"
FT repeat_region 202..477
FT /rpt_family="Alu"
[Part of this file has been deleted for brevity]
ttttgttttt agcttcagcg agaacccaga cctttcccaa agctcaggat tcttcgaaaa 15660
gttgagaaaa ttgatgactt caaagctgaa gactttcaga ttgaagggta caatccgcat 15720
ccaactatta aaatggaaat ggctgtttag ggtgctttca aaggagctcg aaggatattg 15780
tcagtcttta ggggttgggc tggatgccga ggtaaaagtt ctttttgctc taaaagaaaa 15840
aggaactagg tcaaaaatct gtccgtgacc tatcagttat taatttttaa ggatgttgcc 15900
actggcaaat gtaactgtgc cagttctttc cataataaaa ggctttgagt taactcactg 15960
agggtatctg acaatgctga ggttatgaac aaagtgagga gaatgaaatg tatgtgctct 16020
tagcaaaaac atgtatgtgc atttcaatcc cacgtactta taaagaaggt tggtgaattt 16080
cacaagctat ttttggaata tttttagaat attttaagaa tttcacaagc tattccctca 16140
aatctgaggg agctgagtaa caccatcgat catgatgtag agtgtggtta tgaactttaa 16200
agttatagtt gttttatatg ttgctataat aaagaagtgt tctgcattcg tccacgcttt 16260
gttcattctg tactgccact tatctgctca gttccttcct aaaatagatt aaagaactct 16320
ccttaagtaa acatgtgctg tattctggtt tggatgctac ttaaaagagt atattttaga 16380
aataatagtg aatatatttt gccctatttt tctcatttta actgcatctt atcctcaaaa 16440
tataatgacc atttaggata gagttttttt tttttttttt taaactttta taaccttaaa 16500
gggttatttt aaaataatct atggactacc attttgccct cattagcttc agcatggtgt 16560
gacttctcta ataatatgct tagattaagc aaggaaaaga tgcaaaacca cttcggggtt 16620
aatcagtgaa atatttttcc cttcgttgca taccagatac ccccggtgtt gcacgactat 16680
ttttattctg ctaatttatg acaagtgtta aacagaacaa ggaattattc caacaagtta 16740
tgcaacatgt tgcttatttt caaattacag tttaatgtct aggtgccagc ccttgatata 16800
gctatttttg taagaacatc ctcctggact ttgggttagt taaatctaaa cttatttaag 16860
gattaagtag gataacgtgc attgatttgc taaaagaatc aagtaataat tacttagctg 16920
attcctgagg gtggtatgac ttctagctga actcatcttg atcggtagga ttttttaaat 16980
ccatttttgt aaaactattt ccaagaaatt ttaagccctt tcacttcaga aagaaaaaag 17040
ttgttggggc tgagcactta attttcttga gcaggaagga gtttcttcca aacttcacca 17100
tctggagact ggtgtttctt tacagattcc tccttcattt ctgttgagta gccgggatcc 17160
tatcaaagac caaaaaaatg agtcctgtta acaaccacct ggaacaaaaa cagattttat 17220
gcatttatgc tgctccaaga aatgctttta cgtctaagcc agaggcaatt aattaatttt 17280
tttttttttg acatggagtc actgtccgtt gcccaggctg cagtgcagtg gcgcaatctt 17340
ggctcactgc aacctccacc tcccaggttc aagtgattct cctgcctcag cctcccatgt 17400
agctgggatc acaggcacct gccaccatgc ccggctaatt ttttgtattt tttgtagaga 17460
cagggtttca ccatgttggc caggctggtc tcaaacacct gacctcaaat gatccacctg 17520
cctcagcctc ccaaagtgtt gggattacag gcgtaagcca ccatgcccag ccctgaatta 17580
atatttttaa aataagtttg gagactgttg gaaataatag ggcagaggaa catattttac 17640
tggctacttg ccagagttag ttaactcatc aaactctttg ataatagttt gacctctgtt 17700
ggtgaaaatg agccatgatc tcttgaacat gatcagaata aatgccccag ccacacaatt 17760
gtagtccaaa ctttttaggt cactaacttg ctagatggtg ccaggttttt ttgcacaagg 17820
agtgcaaatg ttaagatctc cactagtgag gaaaggctag tattacagaa gccttgtcag 17880
aggcaattga acctccaagc cctggccctc aggcctgagg attttgatac agacaaactg 17940
aagaaccgtt tgttagtgga tattgcaaac aaacaggagt caaagcttgg tgctccacag 18000
tctagttcac gagacaggcg tggcagtggc tggcagcatc tcttctcaca ggggccctca 18060
ggcacagctt accttgggag gcatgtagga agcccgctgg atcatcacgg gatacttgaa 18120
atgctcatgc aggtggtcaa catactcaca caccctagga ggagggaatc agatcggggc 18180
aatgatgcct gaagtcagat tattcacgtg gtgctaactt aaagcagaag gagcgagtac 18240
cactcaattg acagtgttgg ccaaggctta gctgtgttac catgcgtttc taggcaagtc 18300
cctaaacctc tgtgcctcag gtccttttct tctaaaatat agcaatgtga ggtggggact 18360
ttgatgacat gaacacacga agtccctctg agaggttttg tggtgccctt taaaagggat 18420
caattcagac tctgtaaata tccagaatta tttgggttcc tctggtcaaa agtcagatga 18480
atagattaaa atcaccacat tttgtgatct atttttcaag aagcgtttgt attttttcat 18540
atggctgcag cagctgccag gggcttgggg tttttttggc aggtagggtt gggagg 18596
//
Output file format
palindrome writes a text report of the alignment.
Output files for usage example
File: d00596.pal
Palindromes of: D00596
Sequence length is: 18596
Start at position: 1
End at position: 18596
Minimum length of Palindromes is: 15
Maximum length of Palindromes is: 100
Maximum gap between elements is: 100
Number of mismatches allowed in Palindrome: 0
Palindromes:
126 caaaaaaaaaaaaaaaa 142
|||||||||||||||||
217 gtttttttttttttttt 201
127 aaaaaaaaaaaaaaaa 142
||||||||||||||||
215 tttttttttttttttt 200
127 aaaaaaaaaaaaaaaa 142
||||||||||||||||
214 tttttttttttttttt 199
127 aaaaaaaaaaaaaaaa 142
||||||||||||||||
213 tttttttttttttttt 198
127 aaaaaaaaaaaaaaaa 142
||||||||||||||||
212 tttttttttttttttt 197
127 aaaaaaaaaaaaaaaa 142
||||||||||||||||
211 tttttttttttttttt 196
127 aaaaaaaaaaaaaaaa 142
||||||||||||||||
210 tttttttttttttttt 195
127 aaaaaaaaaaaaaaaa 142
||||||||||||||||
209 tttttttttttttttt 194
127 aaaaaaaaaaaaaaaa 142
||||||||||||||||
208 tttttttttttttttt 193
127 aaaaaaaaaaaaaaaa 142
||||||||||||||||
207 tttttttttttttttt 192
127 aaaaaaaaaaaaaaaa 142
||||||||||||||||
206 tttttttttttttttt 191
127 aaaaaaaaaaaaaaaa 142
||||||||||||||||
205 tttttttttttttttt 190
127 aaaaaaaaaaaaaaaagaccgccagggct 155
|||||||||||||||||||||||||||||
204 ttttttttttttttttctggcggtcccga 176
Data files
None.
Notes
Secondary structures-like inverted repeats in genomic sequences may be
implicated in initiation of DNA replication.
Some genomic sequence entries in the databases are composed of
unfinished, draft sequence with gaps of unknown size between contigs.
The positions of these gaps are often indicated by runs of 200 'N'
characters. To prevent palindrome producing large, uninformative
outputs, any palindromes found that are composed only of N will not be
reported.
Unless the qualifier -nooverlap is specified, palindrome makes no
attempt to exclude subsets of previously found palindromes.
References
Some references on inverted repeats:
1. Pearson CE, Zorbas H, Price GB, Zannis-Hadjopoulos M Inverted
repeats, stem-loops, and cruciforms: significance for initiation of
DNA replication. J Cell Biochem 1996 Oct;63(1):1-22
2. Waldman AS, Tran H, Goldsmith EC, Resnick MA. q Long inverted
repeats are an at-risk motif for recombination in mammalian cells.
Genetics. 1999 Dec;153(4):1873-83. PMID: 10581292; UI: 20050682
3. Jacobsen SE Gene silencing: Maintaining methylation patterns. Curr
Biol 1999 Aug 26;9(16):R617-9
4. Lewis S, Akgun E, Jasin M. Palindromic DNA and genome stability.
Further studies. Ann N Y Acad Sci. 1999 May 18;870:45-57. PMID:
10415472; UI: 99343961
5. Dai X, Greizerstein MB, Nadas-Chinni K, Rothman-Denes LB
Supercoil-induced extrusion of a regulatory DNA hairpin. Proc Natl
Acad Sci U S A 1997 Mar 18;94(6):2174-9
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with a status of 0.
Known bugs
None.
See also
Program name Description
einverted Find inverted repeats in nucleotide sequences
equicktandem Find tandem repeats in nucleotide sequences
etandem Find tandem repeats in a nucleotide sequence
einverted also looks for inverted repeats but is much slower and more
sensitive, as it finds low-quality (very mismatched) repeats and
repeats with gaps.
Author(s)
Mark Faller formerly at:
HGMP-RC, 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 (1999) - Mark Faller.
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
|
