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Reverse reverses and/or complements a sequence.
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.
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 *)
%
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
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.
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.
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<
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
None.
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.
doesn't complement the strand.
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