
                               EMBOSS: revseq
     _________________________________________________________________
   
                                Program revseq
                                       
Function

   Reverse and complement a sequence
   
Description

   This takes a sequence and outputs the reverse complement (also known
   as the anti-sense or reverse sense) sequence.
   
   It can also output just the reversed sequence or just the complement
   of the sequence.
   
Usage

   To create the reverse sense of the sequence 'rcr.seq' and output to
   the file 'rcr.rev':
% revseq rcr.seq rcr.rev

   To create the complement of the sequence 'rcr.seq' and output to the
   file 'rcr.rev':
% revseq rcr.seq rcr.rev -norev

   To create the reverse of the sequence 'rcr.seq' and output to the file
   'rcr.rev':
% revseq rcr.seq rcr.rev -nocomp

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outseq]            seqoutall  Output sequence(s) USA

   Optional qualifiers: (none)
   Advanced qualifiers:
   -[no]reverse        bool       Set this to be false if you do not wish to
                                  reverse the output sequence
   -[no]complement     bool       Set this to be false if you do not wish to
                                  complement the output sequence

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-outseq]
   (Parameter 2) Output sequence(s) USA Writeable sequence(s)
   <sequence>.format
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -[no]reverse Set this to be false if you do not wish to reverse the
   output sequence Yes/No Yes
   -[no]complement Set this to be false if you do not wish to complement
   the output sequence Yes/No Yes
   
Input file format

   The input sequence can be one or more sequences.
   
Output file format

   One or more sequences are written out.
   
Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

   It always exits with status 0.
   
Known bugs

   Bugs noted but not yet fixed.
   
   None.
   
See also

   Program name                          Description
   biosed       Replace or delete sequence sections
   cutseq       Removes a specified section from a sequence
   degapseq     Removes gap characters from sequences
   descseq      Alter the name or description of a sequence
   entret       Reads and writes (returns) flatfile entries
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Writes a list file of the logical OR of two sets of sequences
   maskfeat     Mask off features of a sequence
   maskseq      Mask off regions of a sequence
   newseq       Type in a short new sequence
   noreturn     Removes carriage return from ASCII files
   notseq       Excludes a set of sequences and writes out the remaining ones
   nthseq       Writes one sequence from a multiple set of sequences
   pasteseq     Insert one sequence into another
   seqret       Reads and writes (returns) sequences
   seqretsplit  Reads and writes (returns) sequences in individual files
   splitter     Split a sequence into (overlapping) smaller sequences
   swissparse   Retrieves sequences from swissprot using keyword search
   trimest      Trim poly-A tails off EST sequences
   trimseq      Trim ambiguous bits off the ends of sequences
   union        Reads sequence fragments and builds one sequence
   vectorstrip  Strips out DNA between a pair of vector sequences
   yank         Reads a sequence range, appends the full USA to a list file
   
Author(s)

   This application was written by Gary Williams
   (gwilliam@hgmp.mrc.ac.uk)
   
History

   Completed 26 Jan 1999
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
