
                                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     1566
0
     gttgagaaaa ttgatgactt caaagctgaa gactttcaga ttgaagggta caatccgcat     1572
0
     ccaactatta aaatggaaat ggctgtttag ggtgctttca aaggagctcg aaggatattg     1578
0
     tcagtcttta ggggttgggc tggatgccga ggtaaaagtt ctttttgctc taaaagaaaa     1584
0
     aggaactagg tcaaaaatct gtccgtgacc tatcagttat taatttttaa ggatgttgcc     1590
0
     actggcaaat gtaactgtgc cagttctttc cataataaaa ggctttgagt taactcactg     1596
0
     agggtatctg acaatgctga ggttatgaac aaagtgagga gaatgaaatg tatgtgctct     1602
0
     tagcaaaaac atgtatgtgc atttcaatcc cacgtactta taaagaaggt tggtgaattt     1608
0
     cacaagctat ttttggaata tttttagaat attttaagaa tttcacaagc tattccctca     1614
0
     aatctgaggg agctgagtaa caccatcgat catgatgtag agtgtggtta tgaactttaa     1620
0
     agttatagtt gttttatatg ttgctataat aaagaagtgt tctgcattcg tccacgcttt     1626
0
     gttcattctg tactgccact tatctgctca gttccttcct aaaatagatt aaagaactct     1632
0
     ccttaagtaa acatgtgctg tattctggtt tggatgctac ttaaaagagt atattttaga     1638
0
     aataatagtg aatatatttt gccctatttt tctcatttta actgcatctt atcctcaaaa     1644
0
     tataatgacc atttaggata gagttttttt tttttttttt taaactttta taaccttaaa     1650
0
     gggttatttt aaaataatct atggactacc attttgccct cattagcttc agcatggtgt     1656
0
     gacttctcta ataatatgct tagattaagc aaggaaaaga tgcaaaacca cttcggggtt     1662
0
     aatcagtgaa atatttttcc cttcgttgca taccagatac ccccggtgtt gcacgactat     1668
0
     ttttattctg ctaatttatg acaagtgtta aacagaacaa ggaattattc caacaagtta     1674
0
     tgcaacatgt tgcttatttt caaattacag tttaatgtct aggtgccagc ccttgatata     1680
0
     gctatttttg taagaacatc ctcctggact ttgggttagt taaatctaaa cttatttaag     1686
0
     gattaagtag gataacgtgc attgatttgc taaaagaatc aagtaataat tacttagctg     1692
0
     attcctgagg gtggtatgac ttctagctga actcatcttg atcggtagga ttttttaaat     1698
0
     ccatttttgt aaaactattt ccaagaaatt ttaagccctt tcacttcaga aagaaaaaag     1704
0
     ttgttggggc tgagcactta attttcttga gcaggaagga gtttcttcca aacttcacca     1710
0
     tctggagact ggtgtttctt tacagattcc tccttcattt ctgttgagta gccgggatcc     1716
0
     tatcaaagac caaaaaaatg agtcctgtta acaaccacct ggaacaaaaa cagattttat     1722
0
     gcatttatgc tgctccaaga aatgctttta cgtctaagcc agaggcaatt aattaatttt     1728
0
     tttttttttg acatggagtc actgtccgtt gcccaggctg cagtgcagtg gcgcaatctt     1734
0
     ggctcactgc aacctccacc tcccaggttc aagtgattct cctgcctcag cctcccatgt     1740
0
     agctgggatc acaggcacct gccaccatgc ccggctaatt ttttgtattt tttgtagaga     1746
0
     cagggtttca ccatgttggc caggctggtc tcaaacacct gacctcaaat gatccacctg     1752
0
     cctcagcctc ccaaagtgtt gggattacag gcgtaagcca ccatgcccag ccctgaatta     1758
0
     atatttttaa aataagtttg gagactgttg gaaataatag ggcagaggaa catattttac     1764
0
     tggctacttg ccagagttag ttaactcatc aaactctttg ataatagttt gacctctgtt     1770
0
     ggtgaaaatg agccatgatc tcttgaacat gatcagaata aatgccccag ccacacaatt     1776
0
     gtagtccaaa ctttttaggt cactaacttg ctagatggtg ccaggttttt ttgcacaagg     1782
0
     agtgcaaatg ttaagatctc cactagtgag gaaaggctag tattacagaa gccttgtcag     1788
0
     aggcaattga acctccaagc cctggccctc aggcctgagg attttgatac agacaaactg     1794
0
     aagaaccgtt tgttagtgga tattgcaaac aaacaggagt caaagcttgg tgctccacag     1800
0
     tctagttcac gagacaggcg tggcagtggc tggcagcatc tcttctcaca ggggccctca     1806
0
     ggcacagctt accttgggag gcatgtagga agcccgctgg atcatcacgg gatacttgaa     1812
0
     atgctcatgc aggtggtcaa catactcaca caccctagga ggagggaatc agatcggggc     1818
0
     aatgatgcct gaagtcagat tattcacgtg gtgctaactt aaagcagaag gagcgagtac     1824
0
     cactcaattg acagtgttgg ccaaggctta gctgtgttac catgcgtttc taggcaagtc     1830
0
     cctaaacctc tgtgcctcag gtccttttct tctaaaatat agcaatgtga ggtggggact     1836
0
     ttgatgacat gaacacacga agtccctctg agaggttttg tggtgccctt taaaagggat     1842
0
     caattcagac tctgtaaata tccagaatta tttgggttcc tctggtcaaa agtcagatga     1848
0
     atagattaaa atcaccacat tttgtgatct atttttcaag aagcgtttgt attttttcat     1854
0
     atggctgcag cagctgccag gggcttgggg tttttttggc aggtagggtt gggagg         1859
6
//

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:
    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    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
