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 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 

   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
   -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 dying program messages

Standard (Mandatory) qualifiers Allowed values Default
[-sequence]
(Parameter 1)		 Nucleotide sequence(s) filename and optional format, or reference (input 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 <*>.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: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   14-NOV-2006 (Rel. 89, Last updated, Version 3)
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; 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   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
CC   Phone:  +81-559-72-2732
CC   Fax:    +81-559-71-3651
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_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: 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

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:
  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 nameDescription
einverted Finds DNA inverted repeats
equicktandem Finds tandem repeats
etandem Looks for 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 (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