Ereverse

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EREVERSE

FUNCTION

EReverse reverses and/or complements a sequence. EReverse is a version of GCG's Reverse with command line control.

DESCRIPTION

EReverse complements and/or reverses the symbols in a sequence. The complements of all of the supported IUB nucleic acid symbols are listed in Appendix III. The output is written into a new sequence file.

AUTHOR

This GCG program was modified by Jaakko Hattula (Tampere University of Technology, Finland) and 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

The file test.seq contains all of the legitimate GCG sequence characters. Here is a session using EReverse to show how they would look on the opposite strand: 

  
  
  % ereverse
  
   EREVERSE uses nucleotide sequence data
  
   EREVERSE of what sequence ?  gamma.seq
  
                 Start (* 1 *) ?
               End (* 11375 *) ?
  
   Do you want to:
  
    1) reverse only
    2) complement only
    3) reverse and complement
  
   Please choose one (* 3 *):
  
   What should I call the output file (* gamma.rev *)
  
  %

OUTPUT

Here is the output file test.rev: 

  
  
    REVERSE-COMPLEMENT of: gamma.seq  check: 6474  from: 1  to: 11375
  
  Human fetal beta globins G and A gamma
  from Shen, Slightom and Smithies,  Cell 26; 191-203.
  Analyzed by Smithies et al. Cell 26; 345-353.
  
  gamma.rev  Length: 11375  March 19, 1996 14:12  Type: N  Check: 3374  ..
  
    1  GAATTCGGCA GTTACTGCAA CTTCCACTTT TCTCTCACCC GCTCCAGGAA
  
   51  AAGTGACCTG CAGTCACTTT CCTGGTAGTA TTGATTCTTT CTTGTTTGTG
  
  101  GCTGTTCCCC ATTTCCAATT GTTTTCCATG ATTATTGCTT CTACTGTGAT
  
  
            /////////////////////////////////////
  
11251  CCTCAGGTGA TCTGCCTGCC TTGGCCTCCC AAAATTCTGG GATTACAGGC
  
11301  GTGAGCCACC ACTCCCAGCC TCTAAACAAG TGAATCTTAA TTGCTCCTCC
  
11351  TCAGACTAAG GAATATCTAG GATCC

RESTRICTIONS

A reversed sequence is renumbered so that the first base corresponds to the last base of the range you chose. It only makes sense to complement nucleotide sequences! If you don't reverse and complement a sequence, you are in danger of having the sequence in 3' to 5' orientation. All GCG programs and all databases assume that nucleotide sequences are in 5' to 3' order, so be careful. Peptide sequences are generally kept in amino-to-carboxyl orientation. Many legitimate sequence symbols are not IUB-supported nucleic acid symbols, so they have no sensible complement (see Appendix III) .

Embedded comments are lost.

INPUT FILE

Here is the input file test.seq used in the example above: 

  
  
  This sequence contains every symbol in the alphabet of
  legitimate GCG sequence characters (Appendix III).
  
  Test.Seq  Length: 389  July 19, 1994 15:05  Type: N  Check: 8468  ..
  
    1
       >starts with the codons from appendix iii>
       GCTGCCGCAG CGGCXGATGA CAATAACRAY TGTTGCTGYG ATGACGAYGA
  
   51  AGAGGARTTT TTCTTYGGTG GCGGAGGGGG XCATCACCAY ATTATCATAA
  
  101  THAAAAAGAA RTTGTTACTT CTCCTACTGT TRCTXYTAYT GYTRYTXATG
  
  151  AATAACAAYC CTCCCCCACC GCCXCAACAG CARCGTCGCC GACGGCGGAG
  
  201  AAGGCGXAGR MGAMGGMGRM GXTCTTCCTC ATCGAGTAGC TCXAGYWSXA
  
  251  CTACCACAAC GACXGTTGTC GTAGTGGTXT GGXXXTATTA CTAYGAAGAG
  
  301  CAACAGSART AATAGTGATA RTRATRR
                                    >continues with all
       uppercase sequence characters>
                                    ABC DEFGHIJKLM NOPQRSTUVW
  
  351  XYZ.+@&*ab cdefghijkl mnopqrstuv wxyz*@&+.
  
                                                 
 
 


COMMAND-LINE SUMMARY

 
 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.
 


  
  
  Minimal Syntax: % ereverse [-INfile=]ggamma.seq -Default
  
  Prompted Parameters:
  
  -BEGin=1 -END=1700      range of interest
  -REVerse                reverse the strand
  -COMPlement             complement the strand
  [-OUTfile=]ggamma.rev   output file name
  
  Local Data Files: None
  
  Optional Parameters: None
  


 
 


LOCAL DATA FILES

 
 None.

 


OPTIONAL PARAMETERS

 
 None.

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