EMBOSS: pasteseq

Program pasteseq ( YMBC , NCHC )


Insert one sequence into another


This simple editing program allows you to insert one sequence into another sequence after a specified position and to then write out the results to a sequence file.


To insert the sequence 'tst.seq' after position 67 in sequence 'ese.seq' and write the results to the file 'estste.seq':
% pasteseq ese.seq tst.seq estste.seq -pos=67

This is probably slightly more readable if the argument names are used instead of relying on the parameter positions:

% pasteseq -seq=ese.seq -ins=tst.seq -out=estste.seq -pos=67

To insert the sequence 'tst.seq' before the start of sequence 'ese.seq' use -pos=0 :

% pasteseq -seq=ese.seq -ins=tst.seq -out=estste.seq -pos=0

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
  [-insseq]            sequence   Sequence to insert
  [-outseq]            seqout     Output sequence USA
   -pos                integer    The position in the main input sequence to
                                  insert after.
                                  To insert before the start use the position

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   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
(Parameter 1)
Sequence USA Readable sequence Required
(Parameter 2)
Sequence to insert Readable sequence Required
(Parameter 3)
Output sequence USA Writeable sequence <sequence>.format
-pos The position in the main input sequence to insert after. To insert before the start use the position 0. Integer 0 or more $(sequence.end)
Optional qualifiers Allowed values Default
Advanced qualifiers Allowed values Default

Input file format

The sequence and the sequence to insert into it are both single sequence.

Output file format

Single sequence file.

Data files



This can be used as a simple sequence editor.





Diagnostic Error Messages


Exit status

It always exits with status 0.

Known bugs


See also

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
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
revseqReverse and complement a sequence
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


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


Completed 26 Jan 1999

Target users

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