EMBOSS: palindrome manual

palindrome

Function

Looks for inverted repeats in a nucleotide sequence

Description

palindrome looks for inverted repeats (stem loops) in a nucleotide sequence.

It will find inverted repeats that include a proportion of mismatches and gaps (bulges in the stem loop).

It works by finding 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.

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's will not be reported.

Usage

Here is a sample session with palindrome


% palindrome 
Looks for inverted repeats in a nucleotide sequence
Input sequence(s): tembl:hsts1
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 [hsts1.pal]: 
Report overlapping matches [Y]:

Go to the input files for this example
Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
   -minpallen          integer    Enter minimum length of palindrome
   -maxpallen          integer    Enter maximum length of palindrome
   -gaplimit           integer    Enter maximum gap between repeated regions
   -nummismatches      integer    Number of mismatches allowed
  [-outfile]           outfile    Output file name
   -[no]overlap        boolean    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
   -sformat1            string     Input sequence format
   -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 standard output
   -filter              boolean    Read standard input, write 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. 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 deaths

Standard (Mandatory) qualifiers		Allowed values	Default
[-sequence] (Parameter 1)	Sequence database USA	Readable sequence(s)	Required
-minpallen	Enter minimum length of palindrome	Integer 1 or more	10
-maxpallen	Enter maximum length of palindrome	Any integer value	100
-gaplimit	Enter maximum gap between repeated regions	Integer 0 or more	100
-nummismatches	Number of mismatches allowed	Positive integer	0
[-outfile] (Parameter 2)	Output file name	Output file	<sequence>.palindrome
-[no]overlap	Report overlapping matches	Boolean value Yes/No	Yes
Additional (Optional) qualifiers		Allowed values	Default
(none)
Advanced (Unprompted) qualifiers		Allowed values	Default
(none)

Input file format

palindrome reads normal nucleotide sequence USAs.

Input files for usage example

'tembl:hsts1' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:hsts1

ID   HSTS1      standard; DNA; HUM; 18596 BP.
XX
AC   D00596;
XX
SV   D00596.1
XX
DT   17-JUL-1991 (Rel. 28, Created)
DT   27-OCT-1998 (Rel. 57, Last updated, Version 2)
XX
DE   Homo sapiens gene for thymidylate synthase, exons 1, 2, 3, 4, 5, 6, 7,
DE   complete cds.
XX
KW   thymidylate syntase.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-18596
RX   MEDLINE; 91056070.
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. 265:20277-20284(1990).
XX
DR   SWISS-PROT; P04818; TYSY_HUMAN.
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
CC   Phone:  +81-559-72-2732
CC   Fax:    +81-559-71-3651
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..18596
FT                   /chromosome="18"
FT                   /db_xref="taxon:9606"
FT                   /sequenced_mol="DNA"
FT                   /organism="Homo sapiens"
FT                   /clone="lambdaHTS-1 and lambdaHTS-3"
FT                   /map="18p11.32"
FT   repeat_unit     1..148
FT                   /note="Alu sequence"
FT   repeat_unit     202..477


  [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

Output files for usage example

File: hsts1.pal

Palindromes of:  HSTS1 
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

Unless the qualifier '-nooverlap' is specified, palindrome makes no attempt to exclude subsets of previously found palindromes.

Several examples can be seen in the sample output above.

References

Some references on inverted repeats:

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
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
Jacobsen SE Gene silencing: Maintaining methylation patterns. Curr Biol 1999 Aug 26;9(16):R617-9
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
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.

Program name	Description
einverted	Finds DNA inverted repeats
equicktandem	Finds tandem repeats
etandem	Looks for tandem repeats in a nucleotide sequence

Author(s)

Mark Faller (current e-mail address unknown)
while he was with:
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

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

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: tembl:hsts1

Output file format

Output files for usage example

File: hsts1.pal

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments