EMBOSS: palindrome

| ## EMBOSS: palindrome

# Program palindrome

## Function

Looks for inverted repeats in a nucleotide sequence

## Description

This 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.

## Usage

Here is a sample session with palindrome. As there are a number of overlapping possibilties in this sequence, we choose a longer minimum repeat length.

    % palindrome
    Input sequence: embl: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]:

## Command line arguments

       Mandatory qualifiers:
      [-insequence]        sequence   Sequence 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        bool       Report overlapping matches

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-insequence] (Parameter 1) | Sequence USA | Readable sequence | 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 | Yes/No | Yes
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

The input for palindrome is a nucleotide sequence.

## Output file format

Here is the output file from the example run:

    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)

This application was written by Mark Faller (mfaller@hgmp.mrc.ac.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