| 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

       Mandatory qualifiers:
      [-insequence]        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

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       Associated qualifiers:
      "-insequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outfile" related 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-insequence] (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
Optional qualifiers | Allowed values | Default
(none)
Advanced 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:

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 exists 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