Inverted

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INVERTED

INVERTED

FUNCTION

Inverted looks for imperfect inverted repeats in a nucleotide sequence.

AUTHOR

This program was originally written by Richard Durbin and Jean Thierry-Mieg as part of the ACEDB genome database package.

This version was modified for inclusion in EGCG by Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).

EXAMPLE

Here is a sample session with Inverted

  
  
  % inverted
  
   INVERTED uses nucleotide sequence data
  
   INVERTED of what sequence ?  GenEMBL:hsts1
  
                Start (* 1 *) ?
                End (* 18596 *) ?  1000
  
   What gap penalty (* 12 *) ?
  
   What minimum score threshold (* 50 *) ?  35
  
   What match score (* 3 *) ?
  
   What mismatch score (* -4 *) ?
  
   What should I call the output file (* hsts1.inv *) ?
  %

OUTPUT

The output from Inverted is a simple report of hits in the sequence.

  
  
  INVERTED of em_pr:hsts1 check: 1391
  
  Score 236: 108/130 ( 83%) matches, 0 gaps
               .         .         .         .         .
   13 GCTACGCGAGAGGCTGAGGCAGCAGAATTACTTGAACCCAGGAGGCGGAG 62
      |||||  | ||||||||||||| |||||| ||||||||  |||||| |||
  328 CGATGAACCCTCCGACTCCGTCTTCTTAACGAACTTGGACCCTCCGTCTC 279
               .         .         .         .         .
   63 GTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGTGAGAGAG 112
      ||||||||||||| |||||   ||| || ||||||||||||| || ||||
  278 CAACGTCACTCGGTTCTAGGCTGGTAACATGAGGTCGGACCCGCTGTCTC 229
               .         .         .
  113 CGAGACTCTGTCTCAAAAAAAAAAAAAAAA 142
      | ||||| |  |  ||||||||||||||||
  228 GTTCTGACAGGGTTTTTTTTTTTTTTTTTT 199
  
  Score 40: 28/36 ( 77%) matches, 1 gaps
               .         .         .
  853 GGCGGAGCGCGGGACGGCCGCGGGAAAAGGCGCGCGG 889
      ||||| ||| |||||||  || ||  |||  ||||||
  996 CCGCC-CGCCCCCTGCCTCCGTCCGCTTCACCGCGCC 960

INPUT FILE

The input file for Inverted is a GCG nucleotide sequence file.

All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

  
  
  Minimum Syntax: % inverted [-INfile=]GenEmbl:hsldlr02 -Default
  
  Prompted Parameters:
  
  -BEGin=1 -END=100       Range of interest
  [-OUTfile=]hsldlr02.inv  Output file
  -THRESHold=50            Score threshold
  -MATCH=3                 Score for a matching pair of bases
  -MISMATCH=-4             Score for a non-matching pair of bases
  -GAP=12                  Score penalty for a single base gap
  
  Local Data Files: None
  
  Optional Parameters:
  
  -ORIGinal=stdout         Produce original mimimal output format

OPTIONAL PARAMETERS

The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

-ORIGinal=stdout

requests the output format of the original inverted program, optionally with an output file name (the default is to write to the terminal).

Printed: April 22, 1996 15:53 (1162)

Inverted

INVERTED

FUNCTION

DESCRIPTION

Tandem