palindrome

Function

Description

palindrome finds inverted repeats (stem loops) in nucleotide sequences. It will find inverted repeats that include a proportion of mismatches and gaps, that correspond to bulges in the stem loop. It finds 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.

Usage

Command line arguments

Input file format

palindrome reads normal nucleotide sequence USAs.

Output file format

Data files

None.

Notes

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 will not be reported.

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

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.

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)

History

Target users

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