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<HEAD>
  <TITLE>
  EMBOSS: cutseq
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<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">
cutseq
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
    Function
</H2>
Removes a specified section from a sequence
<H2>
    Description
</H2>

This simple editing program allows you to cut out a region from
your sequence by specifying the begin and end positions of the sequence
to remove. 

<p>

It removes the sequence from the specified start to the end positions
(inclusive) and returns the rest of the sequence in the output file. 

<H2>
    Usage
</H2>
<b>Here is a sample session with cutseq</b>
<p>
To remove bases 10 to 12 from a database entry and write to the new sequence file 'gatta2.seq': 
<p>

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

% <b>cutseq tembl:x13776 gatta2.seq -from=10 -to=12 </b>
Removes a specified section from a sequence.

</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>
To remove the first 20 bases from 'tembl:x13776' and write it to 'jsh.seq':  
<p>

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

% <b>cutseq tembl:x13776 -from=1 -to=20 -out=jsh.seq </b>
Removes a specified section from a sequence.

</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>
If the default start and end positions are accepted, then all of the sequence is removed! 
<p>

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

% <b>cutseq tembl:x13776 starta.seq -sbeg=-1000 -send=1290 </b>
Removes a specified section from a sequence.
Start of region to delete [1168]: <b></b>
End of region to delete [1290]: <b></b>

</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:
  [-sequence]          sequence   (Gapped) sequence filename and optional
                                  format, or reference (input USA)
   -from               integer    [Start of sequence (0)] This is the start
                                  position (inclusive) of the section of the
                                  sequence that you wish to remove. (Any
                                  integer value)
   -to                 integer    [End of sequence (0)] This is the end
                                  position (inclusive) of the section of the
                                  sequence that you wish to remove. (Any
                                  integer value)
  [-outseq]            seqout     [<sequence>.<format>] Sequence filename and
                                  optional format (output USA)

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

   "-sequence" 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

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       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>[-sequence]<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>-from</td>
<td>This is the start position (inclusive) of the section of the sequence that you wish to remove.</td>
<td>Any integer value</td>
<td>Start of sequence (0)</td>
</tr>

<tr>
<td>-to</td>
<td>This is the end position (inclusive) of the section of the sequence that you wish to remove.</td>
<td>Any integer value</td>
<td>End of sequence (0)</td>
</tr>

<tr>
<td>[-outseq]<br>(Parameter 2)</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>cutseq</b> reads a single sequence USA.

<p>

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

'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:x13776</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
XX
AC   X13776; M43175;
XX
DT   19-APR-1989 (Rel. 19, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 24)
XX
DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW   aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS   Pseudomonas aeruginosa
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
XX
RN   [1]
RP   1167-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
RN   [2]
RP   1167-2167
RX   DOI; 10.1016/0014-5793(89)80249-2.
RX   PUBMED; 2495988.
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomonas
RT   aeruginosa";
RL   FEBS Lett. 246(1-2):39-43(1989).
XX
RN   [3]
RP   1-1292
RX   PUBMED; 1907262.
RA   Wilson S., Drew R.;
RT   "Cloning and DNA seqence of amiC, a new gene regulating expression of the
RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT   product.";
RL   J. Bacteriol. 173(16):4914-4921(1991).
XX
RN   [4]
RP   1-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
DR   GOA; Q51417.
DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
XX


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

FT                   /replace=""
FT                   /note="ClaI fragment deleted in pSW36,  constitutive
FT                   phenotype"
FT   misc_feature    1
FT                   /note="last base of an XhoI site"
FT   misc_feature    648..653
FT                   /note="end of 658bp XhoI fragment, deletion in  pSW3 causes
FT                   constitutive expression of amiE"
FT   conflict        1281
FT                   /replace="g"
FT                   /citation=[3]
XX
SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
     ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        60
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       120
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       180
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       240
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       300
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       360
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       420
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       480
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       540
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       600
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       660
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       720
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       780
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       840
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       900
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       960
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      1020
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      1080
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      1140
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      1200
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      1260
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      1320
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      1380
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      1440
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      1500
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      1560
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      1620
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      1680
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      1740
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      1800
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      1860
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      1920
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      1980
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      2040
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      2100
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      2160
     cctcgag                                                                2167
//
</pre>
</td></tr></table><p>

<H2>
    Output file format
</H2>

<b>cutseq</b> writes a single sequence file.

<p>

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: gatta2.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;X13776 X13776.1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
ggtaccgctcgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgatcta
cctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcacagg
agaggaaacggatgggatcgcaccaggagcggccgctgatcggcctgctgttctccgaaa
ccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcgagc
aactgaaccgcgagggcggcgtcggcggtcgcccgatcgaaacgctgtcccaggaccccg
gcggcgacccggaccgctatcggctgtgcgccgaggacttcattcgcaaccggggggtac
ggttcctcgtgggctgctacatgtcgcacacgcgcaaggcggtgatgccggtggtcgagc
gcgccgacgcgctgctctgctacccgaccccctacgagggcttcgagtattcgccgaaca
tcgtctacggcggtccggcgccgaaccagaacagtgcgccgctggcggcgtacctgattc
gccactacggcgagcgggtggtgttcatcggctcggactacatctatccgcgggaaagca
accatgtgatgcgccacctgtatcgccagcacggcggcacggtgctcgaggaaatctaca
ttccgctgtatccctccgacgacgacttgcagcgcgccgtcgagcgcatctaccaggcgc
gcgccgacgtggtcttctccaccgtggtgggcaccggcaccgccgagctgtatcgcgcca
tcgcccgtcgctacggcgacggcaggcggccgccgatcgccagcctgaccaccagcgagg
cggaggtggcgaagatggagagtgacgtggcagaggggcaggtggtggtcgcgccttact
tctccagcatcgatacgcccgccagccgggccttcgtccaggcctgccatggtttcttcc
cggagaacgcgaccatcaccgcctgggccgaggcggcctactggcagaccttgttgctcg
gccgcgccgcgcaggccgcaggcaactggcgggtggaagacgtgcagcggcacctgtacg
acatcgacatcgacgcgccacaggggccggtccgggtggagcgccagaacaaccacagcc
gcctgtcttcgcgcatcgcggaaatcgatgcgcgcggcgtgttccaggtccgctggcagt
cgcccgaaccgattcgccccgacccttatgtcgtcgtgcataacctcgacgactggtccg
ccagcatgggcgggggaccgctcccatgagcgccaactcgctgctcggcagcctgcgcga
gttgcaggtgctggtcctcaacccgccgggggaggtcagcgacgccctggtcttgcagct
gatccgcatcggttgttcggtgcgccagtgctggccgccgccggaagccttcgacgtgcc
ggtggacgtggtcttcaccagcattttccagaatggccaccacgacgagatcgctgcgct
gctcgccgccgggactccgcgcactaccctggtggcgctggtggagtacgaaagccccgc
ggtgctctcgcagatcatcgagctggagtgccacggcgtgatcacccagccgctcgatgc
ccaccgggtgctgcctgtgctggtatcggcgcggcgcatcagcgaggaaatggcgaagct
gaagcagaagaccgagcagctccaggaccgcatcgccggccaggcccggatcaaccaggc
caaggtgttgctgatgcagcgccatggctgggacgagcgcgaggcgcaccagcacctgtc
gcgggaagcgatgaagcggcgcgagccgatcctgaagatcgctcaggagttgctgggaaa
cgagccgtccgcctgagcgatccgggccgaccagaacaataacaagaggggtatcgtcat
catgctgggactggttctgctgtacgttggcgcggtgctgtttctcaatgccgtctggtt
gctgggcaagatcagcggtcgggaggtggcggtgatcaacttcctggtcggcgtgctgag
cgcctgcgtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaaggc
cggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagttcct
cgag
</pre>
</td></tr></table><p>

<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: jsh.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;X13776 X13776.1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
tgctcgatcaccaccagccgggcgacgggaactgcacgatctacctggcgagcctggagc
acgagcgggttcgcttcgtacggcgctgagcgacagtcacaggagaggaaacggatggga
tcgcaccaggagcggccgctgatcggcctgctgttctccgaaaccggcgtcaccgccgat
atcgagcgctcgcacgcgtatggcgcattgctcgcggtcgagcaactgaaccgcgagggc
ggcgtcggcggtcgcccgatcgaaacgctgtcccaggaccccggcggcgacccggaccgc
tatcggctgtgcgccgaggacttcattcgcaaccggggggtacggttcctcgtgggctgc
tacatgtcgcacacgcgcaaggcggtgatgccggtggtcgagcgcgccgacgcgctgctc
tgctacccgaccccctacgagggcttcgagtattcgccgaacatcgtctacggcggtccg
gcgccgaaccagaacagtgcgccgctggcggcgtacctgattcgccactacggcgagcgg
gtggtgttcatcggctcggactacatctatccgcgggaaagcaaccatgtgatgcgccac
ctgtatcgccagcacggcggcacggtgctcgaggaaatctacattccgctgtatccctcc
gacgacgacttgcagcgcgccgtcgagcgcatctaccaggcgcgcgccgacgtggtcttc
tccaccgtggtgggcaccggcaccgccgagctgtatcgcgccatcgcccgtcgctacggc
gacggcaggcggccgccgatcgccagcctgaccaccagcgaggcggaggtggcgaagatg
gagagtgacgtggcagaggggcaggtggtggtcgcgccttacttctccagcatcgatacg
cccgccagccgggccttcgtccaggcctgccatggtttcttcccggagaacgcgaccatc
accgcctgggccgaggcggcctactggcagaccttgttgctcggccgcgccgcgcaggcc
gcaggcaactggcgggtggaagacgtgcagcggcacctgtacgacatcgacatcgacgcg
ccacaggggccggtccgggtggagcgccagaacaaccacagccgcctgtcttcgcgcatc
gcggaaatcgatgcgcgcggcgtgttccaggtccgctggcagtcgcccgaaccgattcgc
cccgacccttatgtcgtcgtgcataacctcgacgactggtccgccagcatgggcggggga
ccgctcccatgagcgccaactcgctgctcggcagcctgcgcgagttgcaggtgctggtcc
tcaacccgccgggggaggtcagcgacgccctggtcttgcagctgatccgcatcggttgtt
cggtgcgccagtgctggccgccgccggaagccttcgacgtgccggtggacgtggtcttca
ccagcattttccagaatggccaccacgacgagatcgctgcgctgctcgccgccgggactc
cgcgcactaccctggtggcgctggtggagtacgaaagccccgcggtgctctcgcagatca
tcgagctggagtgccacggcgtgatcacccagccgctcgatgcccaccgggtgctgcctg
tgctggtatcggcgcggcgcatcagcgaggaaatggcgaagctgaagcagaagaccgagc
agctccaggaccgcatcgccggccaggcccggatcaaccaggccaaggtgttgctgatgc
agcgccatggctgggacgagcgcgaggcgcaccagcacctgtcgcgggaagcgatgaagc
ggcgcgagccgatcctgaagatcgctcaggagttgctgggaaacgagccgtccgcctgag
cgatccgggccgaccagaacaataacaagaggggtatcgtcatcatgctgggactggttc
tgctgtacgttggcgcggtgctgtttctcaatgccgtctggttgctgggcaagatcagcg
gtcgggaggtggcggtgatcaacttcctggtcggcgtgctgagcgcctgcgtcgcgttct
acctgatcttttccgcagcagccgggcagggctcgctgaaggccggagcgctgaccctgc
tattcgcttttacctatctgtgggtggccgccaaccagttcctcgag
</pre>
</td></tr></table><p>

<a name="output.3"></a>
<h3>Output files for usage example 3</h3>
<p><h3>File: starta.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;X13776 X13776.1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
</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>

You can delete a complete sequence and write out an empty
sequence file. 

<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="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="pasteseq.html">pasteseq</a></td>
<td>Insert one sequence into another</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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