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)