einverted.txt

emboss的linux版本的源代码

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.fasta

>HSTS1_13_142
gctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcagtga
gccgagatcgcgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaa
aaaaaaaaaa
>HSTS1_199_328
ttttttttttttttttttgggacagtcttgctctgtcgcccaggctggagtacaatggtc
ggatcttggctcactgcaacctctgcctcccaggttcaagcaattcttctgcctcagcct
cccaagtagc
>HSTS1_12128_12301
agaggatttttttttttttttttttttttgagacagagttttgctctgttgcccaggctg
gaatgcaacggcgtgatcttggctcactgtaacctctgcctcctgggttcgagtgattct
cctgcctcagcctccaagtagctgggattacagcatgtgccaccatgcctggct
>HSTS1_12573_12749
agccaggtgtggtggctcacacctgtaattccaacaactccagaggccaaggcgagagga
tcatttgaacccacggaatttgaggctgtagtgagtcatgatcacgccattgcactccat
cctgggcaacagagtgagaccctgaatatttaaaaacaacaacaacaacaaaactct
>HSTS1_12246_12296
ctcctgcctcagcctccaagtagctgggattacagcatgtgccaccatgcc
>HSTS1_13886_13938
ggtatggtggctcatgcctgtaatcccagcactttggaagactgagacaggag
>HSTS1_13884_13949
tgggtatggtggctcatgcctgtaatcccagcactttggaagactgagacaggagcaatt
gcttga
>HSTS1_14628_14692
tcaagcaattcttctgcctcagcctcccaggtagctgggattacaggcacatgccaccac
accca

  File: hsts1.inv


HSTS1: Score 236: 108/130 ( 83%) matches, 0 gaps
      13 gctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcagtgagccgagatcg
cgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaaaaaaaaaaaa 142
         |||||  | ||||||||||||| |||||| ||||||||  |||||| |||||||||||||||| |||||
  ||| || ||||||||||||| || ||||| ||||| |  |  ||||||||||||||||
     328 cgatgaaccctccgactccgtcttcttaacgaacttggaccctccgtctccaacgtcactcggttctagg
ctggtaacatgaggtcggacccgctgtctcgttctgacagggtttttttttttttttttt 199

HSTS1: Score 164: 128/174 ( 73%) matches, 3 gaps
   12128 agaggatttttttttttttttttttttttgagacagagttttgctctgttgcccaggctggaatgcaacg
gcgtgatcttggctcactgtaacctctgcctcc-tgggttcgagtgattctcctgcctcagcctc-caagtagctggga
ttaca-gcatgtgccaccatgcctggct 12301
         ||||  || || || || || |||||    |  ||| || |  |||||||||||||| |||| ||||| |
|||||||| || ||||||  | ||||    ||| ||||||| | |||| |||  ||||  |||||   ||| | ||| |
||||| |  || |||||||  |||||||
   12749 tctcaaaacaacaacaacaacaaaaatttataagtcccagagtgagacaacgggtcctacctcacgttac
cgcactagtactgagtgatgtcggagtttaaggcacccaagtttactaggagagcggaaccggagacctcaacaacctt
aatgtccacactcggtggtgtggaccga 12573

HSTS1: Score 80: 44/51 ( 86%) matches, 2 gaps
   12246 ctcctgcctcag-cctccaagtagctgggattaca-gcatgtgccaccatgcc 12296
         |||||| ||||| | |||||   |||||||||||| ||||| |||||||| ||
   13938 gaggacagagtcagaaggtttcacgaccctaatgtccgtactcggtggtatgg 13886

HSTS1: Score 99: 53/65 ( 81%) matches, 1 gaps
   13884 tgggtatggtggctcatgcctgtaatcccagcactttggaagactgagacaggagcaattgcttga 139
49
         ||||| |||||||   ||||||||||||||||    ||| || ||||| ||| || ||||||||||
   14692 acccacaccaccgtacacggacattagggtcgatggaccctccgactccgtcttc-ttaacgaact 146
28

Data files

   None.

Notes

   Sometimes you can find repeats using the program palindrome that you
   can't find with einverted using the default parameters.

   This is not due to a problem with either program. It is simply because
   some of the shortest repeats that you find with palindrome's default
   parameter values are below einverted's default cutoff score - you
   should decrease the 'Minimum score threshold' to see them.

   For example, when palindrome is run with 'em:hsfau1', it finds the
   repeat:

64    aaaactaaggc    74
      |||||||||||
98    ttttgattccg    88

   einverted will not report this as its score is 33 (11 bases scoring 3
   each, no mismatches or gaps) with is below the default score cutoff of
   50.

   If einverted is run as:

   % einverted em:hsfau1 -threshold 33

   then it will find it:

Score 33: 11/11 (100%) matches, 0 gaps
      64 aaaactaaggc 74
         |||||||||||
      98 ttttgattccg 88

   Anything can be considered to be a repeat if you set the score
   threshold low enough!

   einverted does not report overlapping matches.

   The original "inverted" program was written to annotate the nematode
   genome. Excluding overlapping repeats saved problems with simple
   repeat sequences in this genome.

References

   Some useful 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
   equicktandem Finds tandem repeats
   etandem      Looks for tandem repeats in a nucleotide sequence
   palindrome   Looks for inverted repeats in a nucleotide sequence

   palindrome also looks for inverted repeats but is much faster and less
   sensitive, as it looks for near-perfect repeats.

Author(s)

   This program was originally written by Richard Durbin
   (rd