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  EMBOSS: pasteseq
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<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
pasteseq
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
    Function
</H2>
Insert one sequence into another

<H2>
    Description
</H2>

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.

<H2>
    Usage
</H2>
<b>Here is a sample session with pasteseq</b>
<p>
To insert the sequence 'tsw:flav_nossm' after position 67 in sequence 'tsw:amir_pseae' and write the results to the file 'amir_pseae.fasta':  
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>pasteseq tsw:amir_pseae tsw:flav_nossm -pos=67 </b>
Insert one sequence into another
output sequence [amir_pseae.fasta]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<p>
<b>Example 2</b>
<p>
This does the same thing, but the output qualifier is explicitly used: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>pasteseq tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=67 </b>
Insert one sequence into another

</pre></td></tr></table><p>
<p>
<a href="#output.2">Go to the output files for this example</a><p><p>
<p>
<b>Example 3</b>
<p>
To insert the sequence 'tsw:flav_nossm' before the start of sequence 'tsw:amir_pseae' use -pos=0: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>pasteseq tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=0 </b>
Insert one sequence into another

</pre></td></tr></table><p>
<p>
<a href="#output.3">Go to the output files for this example</a><p><p>


<H2>
    Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   (Gapped) sequence filename and optional
                                  format, or reference (input USA)
  [-bsequence]         sequence   Sequence to insert
   -pos                integer    [$(asequence.end)] The position in the main
                                  input sequence to insert after.
                                  To insert before the start use the position
                                  0. (Integer 0 or more)
  [-outseq]            seqout     [<sequence>.<format>] Sequence filename and
                                  optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-asequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-bsequence" associated qualifiers
   -sbegin2            integer    Start of the sequence to be used
   -send2              integer    End of the sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-outseq" associated qualifiers
   -osformat3          string     Output seq format
   -osextension3       string     File name extension
   -osname3            string     Base file name
   -osdirectory3       string     Output directory
   -osdbname3          string     Database name to add
   -ossingle3          boolean    Separate file for each entry
   -oufo3              string     UFO features
   -offormat3          string     Features format
   -ofname3            string     Features file name
   -ofdirectory3       string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

</pre>
</td></tr></table>
<P>

<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>[-asequence]<br>(Parameter 1)</td>
<td>(Gapped) sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>[-bsequence]<br>(Parameter 2)</td>
<td>Sequence to insert</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>-pos</td>
<td>The position in the main input sequence to insert after.
To insert before the start use the position 0.</td>
<td>Integer 0 or more</td>
<td>$(asequence.end)</td>
</tr>

<tr>
<td>[-outseq]<br>(Parameter 3)</td>
<td>Sequence filename and optional format (output USA)</td>
<td>Writeable sequence</td>
<td><i>&lt;*&gt;</i>.<i>format</i></td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td colspan=4>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td colspan=4>(none)</td>
</tr>

</table>


<H2>
    Input file format
</H2>

<b>pasteseq</b> reads 2 normal sequence USAs.

<p>


<a name="input.1"></a>
<h3>Input files for usage example </h3>

'tsw:amir_pseae' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:amir_pseae</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   AMIR_PSEAE              Reviewed;         196 AA.
AC   P10932;
DT   01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT   08-DEC-2000, sequence version 2.
DT   20-MAR-2007, entry version 55.
DE   Aliphatic amidase regulator.
GN   Name=amiR; OrderedLocusNames=PA3363;
OS   Pseudomonas aeruginosa.
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
OX   NCBI_TaxID=287;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=PAC433;
RX   MEDLINE=89211409; PubMed=2495988; DOI=10.1016/0014-5793(89)80249-2;
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of
RT   Pseudomonas aeruginosa.";
RL   FEBS Lett. 246:39-43(1989).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228;
RX   MEDLINE=20437337; PubMed=10984043; DOI=10.1038/35023079;
RA   Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA   Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA   Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA   Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA   Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T.,
RA   Reizer J., Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT   "Complete genome sequence of Pseudomonas aeruginosa PAO1, an
RT   opportunistic pathogen.";
RL   Nature 406:959-964(2000).
RN   [3]
RP   CHARACTERIZATION.
RX   MEDLINE=95286483; PubMed=7539417;
RA   Wilson S.A., Drew R.E.;
RT   "Transcriptional analysis of the amidase operon from Pseudomonas
RT   aeruginosa.";
RL   J. Bacteriol. 177:3052-3057(1995).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF COMPLEX WITH AMIC.
RC   STRAIN=PAC1;
RX   MEDLINE=99437995; PubMed=10508151; DOI=10.1093/emboj/18.19.5175;
RA   O'Hara B.P., Norman R.A., Wan P.T., Roe S.M., Barrett T.E., Drew R.E.,
RA   Pearl L.H.;
RT   "Crystal structure and induction mechanism of AmiC-AmiR: a ligand-
RT   regulated transcription antitermination complex.";
RL   EMBO J. 18:5175-5186(1999).
CC   -!- FUNCTION: Positive controlling element of amiE, the gene for
CC       aliphatic amidase. Acts as a transcriptional antitermination


<font color=red>  [Part of this file has been deleted for brevity]</font>

CC   -!- SIMILARITY: Contains 1 ANTAR domain.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; X13776; CAA32023.1; -; Genomic_DNA.
DR   EMBL; AE004091; AAG06751.1; -; Genomic_DNA.
DR   PIR; B83226; B83226.
DR   PIR; S03884; S03884.
DR   PDB; 1QO0; X-ray; D/E=1-196.
DR   IntAct; P10932; -.
DR   GenomeReviews; AE004091_GR; PA3363.
DR   KEGG; pae:PA3363; -.
DR   BioCyc; PAER287:PA3363-MONOMER; -.
DR   InterPro; IPR005561; AmiR_NasR_reg.
DR   InterPro; IPR011006; CheY_like.
DR   InterPro; IPR008327; Res_reg_antiterm.
DR   Pfam; PF03861; ANTAR; 1.
DR   PIRSF; PIRSF036382; RR_antiterm; 1.
DR   PROSITE; PS50921; ANTAR; 1.
KW   3D-structure; Complete proteome; Transcription;
KW   Transcription antitermination; Transcription regulation.
FT   CHAIN         1    196       Aliphatic amidase regulator.
FT                                /FTId=PRO_0000064582.
FT   DOMAIN      129    190       ANTAR.
FT   CONFLICT     48     48       S -&gt; A (in Ref. 1).
FT   CONFLICT     64     64       R -&gt; G (in Ref. 1).
FT   CONFLICT    141    141       E -&gt; D (in Ref. 1).
FT   CONFLICT    154    154       A -&gt; V (in Ref. 1).
FT   CONFLICT    170    170       Y -&gt; H (in Ref. 1).
FT   HELIX         3      8
FT   HELIX         9     12
FT   STRAND       14     19
FT   HELIX        23     35
FT   STRAND       38     42
FT   STRAND       54     59
FT   HELIX        65     75
FT   STRAND       81     86
FT   HELIX        91    100
FT   STRAND      103    109
FT   HELIX       112    114
FT   HELIX       115    160
FT   HELIX       164    175
FT   TURN        176    179
FT   HELIX       182    189
SQ   SEQUENCE   196 AA;  21903 MW;  306A4F30E8E4C6C0 CRC64;
     MSANSLLGSL RELQVLVLNP PGEVSDALVL QLIRIGCSVR QCWPPPESFD VPVDVVFTSI
     FQNRHHDEIA ALLAAGTPRT TLVALVEYES PAVLSQIIEL ECHGVITQPL DAHRVLPVLV
     SARRISEEMA KLKQKTEQLQ ERIAGQARIN QAKALLMQRH GWDEREAHQY LSREAMKRRE
     PILKIAQELL GNEPSA
//
</pre>
</td></tr></table><p>
<p><h3>Database entry: tsw:flav_nossm</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   FLAV_NOSSM              Reviewed;          35 AA.
AC   P35707;
DT   01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-1994, sequence version 1.
DT   31-OCT-2006, entry version 30.
DE   Flavodoxin (Fragment).
OS   Nostoc sp. (strain MAC).
OC   Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Nostoc.
OX   NCBI_TaxID=35822;
RN   [1]
RP   PROTEIN SEQUENCE.
RA   Takruri I.A.H., Boulter D., Fitzgerald M.P., Hutber G.N., Rogers L.J.;
RT   "N-terminal amino acid sequences of flavodoxins from Chondrus crispus
RT   and Nostoc strain MAC.";
RL   Phytochemistry 25:2113-2115(1986).
CC   -!- FUNCTION: Low-potential electron donor to a number of redox
CC       enzymes.
CC   -!- COFACTOR: FMN.
CC   -!- SIMILARITY: Belongs to the flavodoxin family.
CC   -!- SIMILARITY: Contains 1 flavodoxin-like domain.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   HSSP; P11241; 1RCF.
DR   InterPro; IPR001226; Flavodoxin.
DR   InterPro; IPR008254; Flavodoxin_1.
DR   Pfam; PF00258; Flavodoxin_1; 1.
DR   PROSITE; PS00201; FLAVODOXIN; 1.
DR   PROSITE; PS50902; FLAVODOXIN_LIKE; 1.
KW   Direct protein sequencing; Electron transport; Flavoprotein; FMN;
KW   Transport.
FT   CHAIN         1    &gt;35       Flavodoxin.
FT                                /FTId=PRO_0000171640.
FT   DOMAIN        4    &gt;35       Flavodoxin-like.
FT   NON_TER      35     35
SQ   SEQUENCE   35 AA;  3820 MW;  B6EEB5CA7A45DDA6 CRC64;
     SKKIGLFYGT ZTGKTESVAE IIDEFGDEVV TLDID
//
</pre>
</td></tr></table><p>

<H2>
    Output file format
</H2>

<b>pasteseq</b> writes a normal sequence file.

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: amir_pseae.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;AMIR_PSEAE Aliphatic amidase regulator.
MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI
FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL
VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG
QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA
</pre>
</td></tr></table><p>

<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: amirplus.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;AMIR_PSEAE Aliphatic amidase regulator.
MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI
FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL
VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG
QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA
</pre>
</td></tr></table><p>

<a name="output.3"></a>
<h3>Output files for usage example 3</h3>
<p><h3>File: amirplus.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;AMIR_PSEAE Aliphatic amidase regulator.
SKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDMSANSLLGSLRELQVLVLNPPGEVS
DALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVAL
VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG
QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA
</pre>
</td></tr></table><p>

<H2>
    Data files
</H2>

None.

<H2>
    Notes
</H2>


	This can be used as a simple sequence editor.

<H2>
    References
</H2>

None.

<H2>
    Warnings
</H2>

None.

<H2>
    Diagnostic Error Messages
</H2>

None.

<H2>
    Exit status
</H2>


	It always exits with status 0.

<H2>
    Known bugs
</H2>


	None.

<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="biosed.html">biosed</a></td>
<td>Replace or delete sequence sections</td>
</tr>

<tr>
<td><a href="codcopy.html">codcopy</a></td>
<td>Reads and writes a codon usage table</td>
</tr>

<tr>
<td><a href="cutseq.html">cutseq</a></td>
<td>Removes a specified section from a sequence</td>
</tr>

<tr>
<td><a href="degapseq.html">degapseq</a></td>
<td>Removes gap characters from sequences</td>
</tr>

<tr>
<td><a href="descseq.html">descseq</a></td>
<td>Alter the name or description of a sequence</td>
</tr>

<tr>
<td><a href="entret.html">entret</a></td>
<td>Reads and writes (returns) flatfile entries</td>
</tr>

<tr>
<td><a href="extractalign.html">extractalign</a></td>
<td>Extract regions from a sequence alignment</td>
</tr>

<tr>
<td><a href="extractfeat.html">extractfeat</a></td>
<td>Extract features from a sequence</td>
</tr>

<tr>
<td><a href="extractseq.html">extractseq</a></td>
<td>Extract regions from a sequence</td>
</tr>

<tr>
<td><a href="listor.html">listor</a></td>
<td>Write a list file of the logical OR of two sets of sequences</td>
</tr>

<tr>
<td><a href="makenucseq.html">makenucseq</a></td>
<td>Creates random nucleotide sequences</td>
</tr>

<tr>
<td><a href="makeprotseq.html">makeprotseq</a></td>
<td>Creates random protein sequences</td>
</tr>

<tr>
<td><a href="maskfeat.html">maskfeat</a></td>
<td>Mask off features of a sequence</td>
</tr>

<tr>
<td><a href="maskseq.html">maskseq</a></td>
<td>Mask off regions of a sequence</td>
</tr>

<tr>
<td><a href="newseq.html">newseq</a></td>
<td>Type in a short new sequence</td>
</tr>

<tr>
<td><a href="noreturn.html">noreturn</a></td>
<td>Removes carriage return from ASCII files</td>
</tr>

<tr>
<td><a href="notseq.html">notseq</a></td>
<td>Exclude a set of sequences and write out the remaining ones</td>
</tr>

<tr>
<td><a href="nthseq.html">nthseq</a></td>
<td>Writes one sequence from a multiple set of sequences</td>
</tr>

<tr>
<td><a href="revseq.html">revseq</a></td>
<td>Reverse and complement a sequence</td>
</tr>

<tr>
<td><a href="seqret.html">seqret</a></td>
<td>Reads and writes (returns) sequences</td>
</tr>

<tr>
<td><a href="seqretsplit.html">seqretsplit</a></td>
<td>Reads and writes (returns) sequences in individual files</td>
</tr>

<tr>
<td><a href="skipseq.html">skipseq</a></td>
<td>Reads and writes (returns) sequences, skipping first few</td>
</tr>

<tr>
<td><a href="splitter.html">splitter</a></td>
<td>Split a sequence into (overlapping) smaller sequences</td>
</tr>

<tr>
<td><a href="trimest.html">trimest</a></td>
<td>Trim poly-A tails off EST sequences</td>
</tr>

<tr>
<td><a href="trimseq.html">trimseq</a></td>
<td>Trim ambiguous bits off the ends of sequences</td>
</tr>

<tr>
<td><a href="union.html">union</a></td>
<td>Reads sequence fragments and builds one sequence</td>
</tr>

<tr>
<td><a href="vectorstrip.html">vectorstrip</a></td>
<td>Strips out DNA between a pair of vector sequences</td>
</tr>

<tr>
<td><a href="yank.html">yank</a></td>
<td>Reads a sequence range, appends the full USA to a list file</td>
</tr>

</table>


<H2>
    Author(s)
</H2>


Gary Williams (gwilliam&nbsp;&copy;&nbsp;rfcgr.mrc.ac.uk)
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK



<H2>
    History
</H2>

Completed 26 Jan 1999

<H2>
    Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.



<H2>
    Comments
</H2>
None

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