
                                 einverted 



Function

   Finds DNA inverted repeats

Description

   einverted looks for inverted repeats (stem loops) in a nucleotide
   sequence.

   It will find inverted repeats that include a proprtion of mismatches
   and gaps (bulges in the stem loop).

Algorithm

   It works by finding alignments between the sequence and its reverse
   complement that exceed a threshold score. Gaps and Mismatches are
   assigned a penalty (negative) score. Matches are assigned a positive
   score. The score is calculated by summing the values of each match,
   the penalties of each mismatch and the large penalties of any gaps.
   Any region whose score exceeds the threshold is reported.

   einverted uses dynamic programming and thus is guaranteed to find the
   optimal alignment, but is slower than, for example, a self-by-self
   BLAST. It can find multiple inverted repeats in a sequence.

   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.

Usage

   Here is a sample session with einverted


% einverted tembl:hsts1 
Finds DNA inverted repeats
Gap penalty [12]: 
Minimum score threshold [50]: 
Match score [3]: 
Mismatch score [-4]: 
Output file [hsts1.inv]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Sequence USA
   -gap                integer    Gap penalty
   -threshold          integer    Minimum score threshold
   -match              integer    Match score
   -mismatch           integer    Mismatch score
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers:
   -maxrepeat          integer    Maximum separation between the start of
                                  repeat and the end of the inverted repeat
                                  (the default is 4000 bases).

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1             integer    Start of the sequence to be used
   -send1               integer    End of the 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 USA Readable sequence Required
   -gap Gap penalty Any integer value 12
   -threshold Minimum score threshold Any integer value 50
   -match Match score Any integer value 3
   -mismatch Mismatch score Any integer value -4
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.einverted
   Additional (Optional) qualifiers Allowed values Default
   -maxrepeat Maximum separation between the start of repeat and the end
   of the inverted repeat (the default is 4000 bases). Any integer value
   4000
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   The input for einverted is a nucleotide sequence

  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.inv


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

Score 228: 108/132 ( 81%) matches, 0 gaps
      11 cagctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcagtgagccgagat
cgcgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaaaaaaaaaaaa 142
           |||||  | ||||||||||||| |||||| ||||||||  |||||| |||||||||||||||| ||||
|   ||| || ||||||||||||| || ||||| ||||| |  |  ||||||||||||||||
     330 accgatgaaccctccgactccgtcttcttaacgaacttggaccctccgtctccaacgtcactcggttcta
ggctggtaacatgaggtcggacccgctgtctcgttctgacagggtttttttttttttttttt 199

Score 226: 110/136 ( 80%) matches, 0 gaps
       7 gtcccagctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcagtgagccg
agatcgcgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaaaaaaaaaaaa 142
         ||    |||||  | ||||||||||||| |||||| ||||||||  |||||| ||||||||||||||||
|||||   ||| || ||||||||||||| || ||||| ||||| |  |  ||||||||||||||||
     334 caccaccgatgaaccctccgactccgtcttcttaacgaacttggaccctccgtctccaacgtcactcggt
tctaggctggtaacatgaggtcggacccgctgtctcgttctgacagggtttttttttttttttttt 199

Score 221: 111/139 ( 79%) matches, 0 gaps
       4 gtagtcccagctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcagtgag
ccgagatcgcgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaaaaaaaaaaaa 142
         |  ||    |||||  | ||||||||||||| |||||| ||||||||  |||||| ||||||||||||||
|| |||||   ||| || ||||||||||||| || ||||| ||||| |  |  ||||||||||||||||
     337 ccgcaccaccgatgaaccctccgactccgtcttcttaacgaacttggaccctccgtctccaacgtcactc
ggttctaggctggtaacatgaggtcggacccgctgtctcgttctgacagggtttttttttttttttttt 199

Score 216: 112/142 ( 78%) matches, 0 gaps
       1 cctgtagtcccagctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcagt
gagccgagatcgcgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaaaaaaaaaaaa 142

         |  |  ||    |||||  | ||||||||||||| |||||| ||||||||  |||||| |||||||||||
||||| |||||   ||| || ||||||||||||| || ||||| ||||| |  |  ||||||||||||||||
     340 gacccgcaccaccgatgaaccctccgactccgtcttcttaacgaacttggaccctccgtctccaacgtca
ctcggttctaggctggtaacatgaggtcggacccgctgtctcgttctgacagggtttttttttttttttttt 199


Score 199: 54/170 ( 31%) matches, 1 gaps
       1 -cctgtagtcccagctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcag
tgagccgagatcgcgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaaaaaaaaaaaagaccgc
cagggctcaaacaaaaaacctc 170
           |||        |        |  |     |    |  | |   |  | || ||  |     | |
     | |     || |  |      |   |  ||          |        |  |||||||||||||||| |
 |     |   ||       ||
     342 tcgacccgcaccaccgatgaaccctccgactccgtcttcttaacgaacttggaccctccgtctccaacgt
cactcggttctaggctggtaacatgaggtcggacccgctgtctcgttctgacagggttttttttttttttttttttttt
tttttctggcggtcccgaaaag 172

Score 175: 56/171 ( 32%) matches, 1 gaps
       1 -cctgtagtcccagctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcag
tgagccgagatcgcgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaaaaaaaaaaaagaccgc
cagggctcaaacaaaaaacctcg 171
              | | |   |   |      ||  |  |  ||||||  | |           || ||  |  |  |
      |  |     | ||     | |  |      |          |        | ||||||||||||||| |
 |      |     |   | |
     344 aatcgacccgcaccaccgatgaaccctccgactccgtcttcttaacgaacttggaccctccgtctccaac
gtcactcggttctaggctggtaacatgaggtcggacccgctgtctcgttctgacagggttttttttttttttttttttt
tttttttctggcggtcccgaaaa 173

Score 172: 100/120 ( 83%) matches, 4 gaps
     345 tttttgtacttttagtagagacgggggtttcaccatgttgtccaggctggtcttgaactcctgacctcag
gtgatccacccgcctcggccccccaaagtactaggattacaggcgtgagccacc 468
         |||||||  | ||||||||||| ||||| || |||||||| |||||||||||   || |||| |||||||
|||||    | | ||| ||| |||||||   | |||||||||||||||||||||
    3177 aaaaacacaataatcatctctgaccccacagcggtacaaccggtccgaccagggtttaaggattggagtc
cacta----gactgagtcggagggtttcgccaccctaatgtccgcactcggtgg 3058

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

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

Score 130: 74/94 ( 78%) matches, 1 gaps
   13890 tggtggctcatgcctgtaatcccagcactttggaagactgagacaggagcaattgcttgaggtctggagt
tcaataccagcctgggcaacataac 13984
         |||||||| ||||||||||| |||| ||||| | || ||||| |||| |  |   ||||| ||| |||||
|  | | |||||||| |||||| ||
   14822 accaccgaatacggacattaaggtcttgaaagcctccgactccgtccaccat-gtgaacttcagtcctca
aactctagtcggaccggttgtactg 14729

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 © sanger.ac.uk)
   Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
   CB10 1SA, UK.

   This application was modified for inclusion in EMBOSS by Peter Rice
   (pmr © ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

   Written (1999) - Peter Rice

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
