REVERSE

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Table of Contents
FUNCTION
DESCRIPTION
EXAMPLE
OUTPUT
INPUT FILES
RESTRICTIONS
INPUT FILE
COMMAND-LINE SUMMARY
LOCAL DATA FILES
PARAMETER REFERENCE

FUNCTION

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Reverse reverses and/or complements a sequence.

DESCRIPTION

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

EXAMPLE

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


% reverse

  REVERSE of what sequence ?  test.seq

                    Begin (* 1 *) ?
                  End (*   389 *) ?

  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 (* test.rev *)

%

OUTPUT

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Here is the output file test.rev:


!!NA_SEQUENCE 1.0
  REVERSE-COMPLEMENT of: test.seq  check: 3365  from: 1  to: 389

This sequence contains every symbol in the alphabet of
legitimate GCG sequence characters (Appendix III).

test.rev  Length: 389  October 21, 1996 10:15  Type: N  Check: 8096  ..

       1  .~....rxwb aasy...nk. m..dc..hgv t...~..RXW BAASY...NK

      51  .M..DC..HG VTYYATYAYT ATCACTATTA YTSCTGTTGC TCTTCRTAGT

     101  AATAXXXCCA XACCACTACG ACAACXGTCG TTGTGGTAGT XSWRCTXGAG

     151  CTACTCGATG AGGAAGAXCK YCKCCKTCKY CTXCGCCTTC TCCGCCGTCG

     201  GCGACGYTGC TGTTGXGGCG GTGGGGGAGG RTTGTTATTC ATXARYARCA

     251  RTARXAGYAA CAGTAGGAGA AGTAACAAYT TCTTTTTDAT TATGATAATR

     301  TGGTGATGXC CCCCTCCGCC ACCRAAGAAA AAYTCCTCTT CRTCGTCATC

     351  RCAGCAACAR TYGTTATTGT CATCXGCCGC TGCGGCAGC

INPUT FILES

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Reverse accepts a single sequence as input. The function of Reverse depends on whether your input sequence(s) are protein or nucleotide. Programs determine the type of a sequence by the presence of either Type: N or Type: P on the last line of the text heading just above the sequence. If your sequence(s) are not the correct type, see Appendix VI for information on how to change or set the type of a sequence.

RESTRICTIONS

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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 IUPAC-IUB-supported nucleic acid symbols, so they have no sensible complement (see Appendix III).

Embedded comments are lost.

INPUT FILE

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


!!NA_SEQUENCE 1.0
This sequence contains every symbol in the alphabet of
legitimate GCG sequence characters (Appendix III).

Test.Seq  Length: 389  September 30, 1998 10:49  Type: N  Check: 3365  ..

       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*@&~.

                                                    <ends with
          all lowercase sequence characters<

COMMAND-LINE SUMMARY

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All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.


Minimal Syntax: % reverse [-INfile=]ggamma.seq

Prompted Parameters:

-BEGin=1 -END=1700      sets the range of interest
-NOREVerse              doesn't reverse the strand
-NOCOMPlement           doesn't complement the strand
[-OUTfile=]ggamma.rev   names the output file

Local Data Files: None

Optional Parameters: None

LOCAL DATA FILES

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None.

PARAMETER REFERENCE

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You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.

-NOCOMPlement

doesn't complement the strand.

Printed: December 9, 1998 16:29 (1162)

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