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 nameDescription
biosedReplace or delete sequence sections
cutseqRemoves a specified section from a sequence
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
infoseqDisplays some simple information about sequences
listorWrites a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExcludes a set of sequences and writes out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
seqretReads and writes (returns) sequences
seqretallReads and writes (returns) a set of sequences one at a time
seqretsetReads and writes (returns) a set of sequences all at once
seqretsplitReads and writes (returns) sequences in individual files
splitterSplit a sequence into (overlapping) smaller sequences
swissparseRetrieves sequences from swissprot using keyword search
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
vectorstripStrips out DNA between a pair of vector sequences

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