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

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



<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Read and write (return) sequences

<H2>
    Description
</H2>


<p><b>seqret</b> reads in one or more sequences and writes them out again. The sequence input may be a literal sequence or read from a database, file, file of sequence names, or even the command-line or the output of another programs. The sequence output can be written to screen, to file, or passed to another program. A wide range of standard sequence formats may be specified for input and output.  If you don't specify the input format, <b>seqret</b> will try a set of possible formats until it reads it in successfully. The sequence input and output, as for all EMBOSS programs, is described by a Uniform Sequence Address.  This is is a very flexible way of specifying one or more sequences from a variety of sources and includes sequence files, database queries and external applications.</p>

<p>There are many options built-in into EMBOSS for detailed specification of the input and output sequences, for example the sequence type, file format. specification of sequence regions by begin and end positions, or generation of the reverse complement of a nucleic acid sequence.  On output <b>seqret</b> can change the case of the sequence to upper or to lower case. </p>

<p><b>seqret</b> is useful for a variety of tasks, including extracting sequences from databases, displaying sequences, reformatting sequences, producing the reverse complement of a sequence, extracting fragments of a sequence, sequence case conversion or any combination of the above functions.</p>




<H2>
    Usage
</H2>
Here is a sample session with <b>seqret</b>
<p>
Extract an entry from a database and write it to a file:  
<p>

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

% <b>seqret </b>
Read and write (return) sequences
Input (gapped) sequence(s): <b>tembl:x65923</b>
output sequence(s) [x65923.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>
Read all entries in the database 'tembl' that start with 'ab' and write them to a file. In this example the specification is all done in the command line and to stop Unix getting confused by the '*' character, it has to have a backslash ('\') before it: 
<p>

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

% <b>seqret "tembl:ab*"  aball.seq </b>
Read and write (return) sequences

</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>
seqret does not read in features by default because this results in slightly faster performance.  If however you wish to read in features with your sequence and write them out on output, using '-feature' will change the default behaviour to use any features present in the sequence.  N.B. use embl format for the output file as the default format 'fasta' reports the features in gff (file "&lt;seqname&gt;.gff") 
<p>

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

% <b>seqret -feature </b>
Read and write (return) sequences
Input (gapped) sequence(s): <b>tembl:x65923</b>
output sequence(s) [x65923.fasta]: <b>embl::x65923.embl</b>

</pre></td></tr></table><p>
<p>
<a href="#output.3">Go to the output files for this example</a><p><p>
<p>
<b>Example 4</b>
<p>
Display the contents of the sequence on the screen: 
<p>

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

% <b>seqret </b>
Read and write (return) sequences
Input (gapped) sequence(s): <b>tembl:x65923</b>
output sequence(s) [x65923.fasta]: <b>stdout</b>

>X65923 X65923.1 H.sapiens fau mRNA
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 5</b>
<p>
Write the result in GCG format by using the qualifier '-osformat'. 
<p>

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

% <b>seqret -osf gcg </b>
Read and write (return) sequences
Input (gapped) sequence(s): <b>tembl:x65923</b>
output sequence(s) [x65923.gcg]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.5">Go to the output files for this example</a><p><p>
<p>
<b>Example 6</b>
<p>
Write the result in GCG format by specifying the format in the output USA on the command line. 
<p>

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

% <b>seqret -outseq gcg::x65923.gcg </b>
Read and write (return) sequences
Input (gapped) sequence(s): <b>tembl:x65923</b>

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 7</b>
<p>
Write the result in GCG format by specifying the format in the output USA at the prompt. 
<p>

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

% <b>seqret </b>
Read and write (return) sequences
Input (gapped) sequence(s): <b>tembl:x65923</b>
output sequence(s) [x65923.fasta]: <b>gcg::x65923.gcg</b>

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 8</b>
<p>
Write the reverse-complement of a sequence: 
<p>

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

% <b>seqret -srev </b>
Read and write (return) sequences
Input (gapped) sequence(s): <b>tembl:x65923</b>
output sequence(s) [x65923.fasta]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.8">Go to the output files for this example</a><p><p>
<p>
<b>Example 9</b>
<p>
Extract the bases between the positions starting at 5 and ending at 25: 
<p>

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

% <b>seqret -sbegin 5 -send 25 </b>
Read and write (return) sequences
Input (gapped) sequence(s): <b>tembl:x65923</b>
output sequence(s) [x65923.fasta]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.9">Go to the output files for this example</a><p><p>
<p>
<b>Example 10</b>
<p>
Extract the bases between the positions starting at 5 and ending at 5 bases before the end of the sequence: 
<p>

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

% <b>seqret -sbegin 5 -send -5 </b>
Read and write (return) sequences
Input (gapped) sequence(s): <b>tembl:x65923</b>
output sequence(s) [x65923.fasta]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.10">Go to the output files for this example</a><p><p>
<p>
<b>Example 11</b>
<p>
Read all entries in the database 'tembl' that start with 'h' and write them to a file: 
<p>

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

% <b>seqret </b>
Read and write (return) sequences
Input (gapped) sequence(s): <b>tembl:h*</b>
output sequence(s) [h45989.fasta]: <b>hall.seq</b>

</pre></td></tr></table><p>
<p>
<a href="#output.11">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>
Read and write (return) sequences
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [<sequence>.<format>] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -feature            boolean    Use feature information
   -firstonly          boolean    [N] Read one sequence and stop

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit

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

<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-sequence]<br>(Parameter 1)</td>
<td>seqall</td>
<td>(Gapped) sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outseq]<br>(Parameter 2)</td>
<td>seqoutall</td>
<td>Sequence set(s) filename and optional format (output USA)</td>
<td>Writeable sequence(s)</td>
<td><i>&lt;*&gt;</i>.<i>format</i></td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-feature</td>
<td>boolean</td>
<td>Use feature information</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-firstonly</td>
<td>boolean</td>
<td>Read one sequence and stop</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-sequence" associated seqall qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sbegin1<br>-sbegin_sequence</td>
<td>integer</td>
<td>Start of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -send1<br>-send_sequence</td>
<td>integer</td>
<td>End of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sreverse1<br>-sreverse_sequence</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sask1<br>-sask_sequence</td>
<td>boolean</td>
<td>Ask for begin/end/reverse</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -snucleotide1<br>-snucleotide_sequence</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sprotein1<br>-sprotein_sequence</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -slower1<br>-slower_sequence</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -supper1<br>-supper_sequence</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -scircular1<br>-scircular_sequence</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -squick1<br>-squick_sequence</td>
<td>boolean</td>
<td>Read id and sequence only</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sformat1<br>-sformat_sequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_sequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ioffset1<br>-ioffset_sequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sdbname1<br>-sdbname_sequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sid1<br>-sid_sequence</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ufo1<br>-ufo_sequence</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fformat1<br>-fformat_sequence</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fopenfile1<br>-fopenfile_sequence</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outseq" associated seqoutall qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osformat2<br>-osformat_outseq</td>
<td>string</td>
<td>Output seq format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osextension2<br>-osextension_outseq</td>
<td>string</td>
<td>File name extension</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osname2<br>-osname_outseq</td>
<td>string</td>
<td>Base file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osdirectory2<br>-osdirectory_outseq</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osdbname2<br>-osdbname_outseq</td>
<td>string</td>
<td>Database name to add</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ossingle2<br>-ossingle_outseq</td>
<td>boolean</td>
<td>Separate file for each entry</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -oufo2<br>-oufo_outseq</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -offormat2<br>-offormat_outseq</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ofname2<br>-ofname_outseq</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ofdirectory2<br>-ofdirectory_outseq</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>


<H2>
    Input file format
</H2>


<b>seqret</b> reads one or more nucleotide or protein sequences.

<p>
<p>

The input is a standard EMBOSS sequence query (also known as a 'USA').

<p>
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl

<p>

Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.

<p>
The input format can be specified by using the
command-line qualifier <tt>-sformat xxx</tt>, where 'xxx' is replaced
by the name of the required format.  The available format names are:
gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
(nbrf), swissprot (swiss, sw), dasgff and debug.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.

<p>


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

'tembl:x65923' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:x65923</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the INSDC.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   PUBMED; 8395683.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR   Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR   Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR   Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR   Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR   Ensembl-Tr; ENST00000531743; Homo_sapiens.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="H-InvDB:HIT000322806.14"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="PDB:2L7R"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
//
</pre>
</td></tr></table><p>

<H2>
    Output file format
</H2>

<p>

The output is a standard EMBOSS sequence file. 

<p>

The results can be output in one of several styles by using the
command-line qualifier <tt>-osformat xxx</tt>, where 'xxx' is replaced by
the name of the required format.  The available format names are: embl,
genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel,
feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.

<p>

<p>

The output from <b>seqret</b> is one or more sequences, and by default will be
written in FASTA format. 

<p>

If the '-firstonly' qualifier is used then only the first sequence of the
input USA specification will be written out. 

<p>

In some cases the output filename will be the same as the input
filename, but as <b>seqret</b> reads only the first sequence before opening
the output file it may try to overwrite the input.  Note that this is
not true of <b>seqretset</b> which reads all sequences into memory at
startup, but which can need a large amount of memory for many sequences.

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: x65923.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;X65923 X65923.1 H.sapiens fau mRNA
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa
</pre>
</td></tr></table><p>

<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: aball.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;AB009602 AB009602.1 Schizosaccharomyces pombe mRNA for MET1 homolog, partial cds.
gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
aacaattctaatggtcaaaaa
&gt;AB000095 AB000095.1 Homo sapiens mRNA for hepatocyte growth factor activator inhibitor, complete cds.
cggccgagcccagctctccgagcaccgggtcggaagccgcgacccgagccgcgcaggaag
ctgggaccggaacctcggcggacccggccccacccaactcacctgcgcaggtcaccagca
ccctcggaacccagaggcccgcgctctgaaggtgacccccctggggaggaaggcgatggc
ccctgcgaggacgatggcccgcgcccgcctcgccccggccggcatccctgccgtcgcctt
gtggcttctgtgcacgctcggcctccagggcacccaggccgggccaccgcccgcgccccc
tgggctgcccgcgggagccgactgcctgaacagctttaccgccggggtgcctggcttcgt
gctggacaccaacgcctcggtcagcaacggagctaccttcctggagtcccccaccgtgcg
ccggggctgggactgcgtgcgcgcctgctgcaccacccagaactgcaacttggcgctagt
ggagctgcagcccgaccgcggggaggacgccatcgccgcctgcttcctcatcaactgcct
ctacgagcagaacttcgtgtgcaagttcgcgcccagggagggcttcatcaactacctcac
gagggaagtgtaccgctcctaccgccagctgcggacccagggctttggagggtctgggat
ccccaaggcctgggcaggcatagacttgaaggtacaaccccaggaacccctggtgctgaa
ggatgtggaaaacacagattggcgcctactgcggggtgacacggatgtcagggtagagag
gaaagacccaaaccaggtggaactgtggggactcaaggaaggcacctacctgttccagct
gacagtgactagctcagaccacccagaggacacggccaacgtcacagtcactgtgctgtc
caccaagcagacagaagactactgcctcgcatccaacaaggtgggtcgctgccggggctc
tttcccacgctggtactatgaccccacggagcagatctgcaagagtttcgtttatggagg
ctgcttgggcaacaagaacaactaccttcgggaagaagagtgcattctagcctgtcgggg
tgtgcaaggcccctccatggaaaggcgccatccagtgtgctctggcacctgtcagcccac
ccagttccgctgcagcaatggctgctgcatcgacagtttcctggagtgtgacgacacccc
caactgccccgacgcctccgacgaggctgcctgtgaaaaatacacgagtggctttgacga
gctccagcgcatccatttccccagtgacaaagggcactgcgtggacctgccagacacagg
actctgcaaggagagcatcccgcgctggtactacaaccccttcagcgaacactgcgcccg
ctttacctatggtggttgttatggcaacaagaacaactttgaggaagagcagcagtgcct
cgagtcttgtcgcggcatctccaagaaggatgtgtttggcctgaggcgggaaatccccat
tcccagcacaggctctgtggagatggctgtcgcagtgttcctggtcatctgcattgtggt
ggtggtagccatcttgggttactgcttcttcaagaaccagagaaaggacttccacggaca
ccaccaccacccaccacccacccctgccagctccactgtctccactaccgaggacacgga
gcacctggtctataaccacaccacccggcccctctgagcctgggtctcaccggctctcac
ctggccctgcttcctgcttgccaaggcagaggcctgggctgggaaaaactttggaaccag
actcttgcctgtttcccaggcccactgtgcctcagagaccagggctccagcccctcttgg
agaagtctcagctaagctcacgtcctgagaaagctcaaaggtttggaaggagcagaaaac
ccttgggccagaagtaccagactagatggacctgcctgcataggagtttggaggaagttg
gagttttgtttcctctgttcaaagctgcctgtccctaccccatggtgctaggaagaggag
tggggtggtgtcagaccctggaggccccaaccctgtcctcccgagctcctcttccatgct
gtgcgcccagggctgggaggaaggacttccctgtgtagtttgtgctgtaaagagttgctt
tttgtttatttaatgctgtggcatgggtgaagaggaggggaagaggcctgtttggcctct
ctgtcctctcttcctcttcccccaagattgagctctctgcccttgatcagccccaccctg


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

ccttgtcaggcggaagggcatcaacggcgggcttctcccgctgggcctgagcccgttgat
ctccccaagctgcaagcgaaccttgcgggtcaaggtcgagggcaatcacggattcccctg
cctctgtggccgcgacggcaatggcagcagcgagggtagtttttcccgcgccgcccttct
gcgtgaccagagcaattgtcttcatgcctgcactatagcattaaggcactaaagcgtcaa
agcgccatagcggcatagcggcatagcggcatagcgctaaaatgctatagcattattaaa
tacagcgctacagcgctataatgctgcaacggttaggaccgcaatttgcgccccgggccg
gttgcgctatcgaccagctcaattaactgctcgggctcggacgcgaaccacgcgaagctg
ccccaagccaaggagtcgagggagccacggttgatgagagctttgttgtaggtggaccag
ttggtgattttgaacttttgctttgccacggaacggtctgcgttgtcgggaagatgcgtg
atctgatccttcaactcagcaaaagttcgatttattcaacaaagccacgttgtgtctcaa
aatctctgatgttacattgcacaagataaaaatatatcatcatgaacaataaaactgtct
gcttacataaacagtaatacaaggggtgttatgagccatattcaacgggaaacgtcttgc
tcgaagccgcgattaaattccaacatggatgctgatttatatgggtataaatgggctcgc
gataatgtcgggcaatcaggtgcgacaatctatcgattgtatgggaagcccgatgcgcca
gagttgtttctgaaacatggcaaaggtagcgttgccaatgatgttacagatgagatggtc
agactaaactggctgacggaatttatgcctcttccgaccatcaagcattttatccgtact
cctgatgatgcatggttactcaccactgcgatccccgggaaaacagcattccaggtatta
gaagaatatcctgattcaggtgaaaatattgttgatgcgctggcagtgttcctgcgccgg
ttgcattcgattcctgtttgtaattgtccttttaacagcgatcgcgtatttcgtctcgct
caggcgcaatcacgaatgaataacggtttggttgatgcgagtgattttgatgacgagcgt
aatggctggcctgttgaacaagtctggaaagaaatgcataagcttttgccattctcaccg
gattcagtcgtcactcatggtgatttctcacttgataaccttatttttgacgaggggaaa
ttaataggttgtattgatgttggacgagtcggaatcgcagaccgataccaggatcttgcc
atcctatggaactgcctcggtgagttttctccttcattacagaaacggctttttcaaaaa
tatggtattgataatcctgatatgaataaattgcagtttcatttgatgctcgatgagttt
ttctaatcagaattggttaattggttgtaacactggcagagcattacgctgacttgacgg
gacggcggctttgttgaataaatcgcattcgccattcaggctgcgcaactgttgggaagg
gcgatcggtgcgggcctcttcgctattacgccagctggcgaaagggggatgtgctgcaag
gcgattaagttgggtaacgccagggttttcccagtcacgacgttgtaaaacgacggccag
tgccaagcttgcatgcctgcaggtcgactctagaggatccccgggtaccgagctcgaatt
cgtaatcatggtcatagctgtttcctgtgtgaaattgttatccgctcacaattccacaca
acatacgagccggaagcataaagtgtaaagcctggggtgcctaatgagtgagctaactca
cattaattgcgttgcgctcactgcccgctttccagtcgggaaacctgtcgtgccagctgc
attaatgaatcggccaacgcgcggggagaggcggtttgcgtattggcgaacttttgctga
gttgaaggatcagatcacgcatcttcccgacaacgcagaccgttccgtggcaaagcaaaa
gttcaaaatcagtaaccgtcagtgccgataagttcaaagttaaacctggtgttgatacca
acattgaaacgctgatcgaaaacgcgctgaaaaacgctgctgaatgtgcgagcttcttcc
gcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagct
cactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatg
tgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttc
cataggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcga
aacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctct
cctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtg
gcgctttctcaatgctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaag
ctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactat
cgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaac
aggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaac
tacggctacactagaaggacagtatttggtatctgcgctctgctgaagccagttaccttc
ggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttt
tttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatc
ttttctacggggtctgacgctcagtggaacgatccgtcga
</pre>
</td></tr></table><p>

<a name="output.3"></a>
<h3>Output files for usage example 3</h3>
<p><h3>File: x65923.embl</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the INSDC.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM.
XX
RN   [2]
RP   1-518
RX   PUBMED; 8395683.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR   Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR   Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR   Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR   Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR   Ensembl-Tr; ENST00000531743; Homo_sapiens.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="H-InvDB:HIT000322806.14"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="PDB:2L7R"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
//
</pre>
</td></tr></table><p>

<a name="output.5"></a>
<h3>Output files for usage example 5</h3>
<p><h3>File: x65923.gcg</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
!!NA_SEQUENCE 1.0

H.sapiens fau mRNA

X65923  Length: 518  Type: N  Check: 2981 ..

   1 ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc

  51 gccaatatgc agctctttgt ccgcgcccag gagctacaca ccttcgaggt

 101 gaccggccag gaaacggtcg cccagatcaa ggctcatgta gcctcactgg

 151 agggcattgc cccggaagat caagtcgtgc tcctggcagg cgcgcccctg

 201 gaggatgagg ccactctggg ccagtgcggg gtggaggccc tgactaccct

 251 ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc

 301 gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag

 351 aagaagaaga agacaggtcg ggctaagcgg cggatgcagt acaaccggcg

 401 ctttgtcaac gttgtgccca cctttggcaa gaagaagggc cccaatgcca

 451 actcttaagt cttttgtaat tctggctttc tctaataaaa aagccactta

 501 gttcagtcaa aaaaaaaa

</pre>
</td></tr></table><p>

<a name="output.8"></a>
<h3>Output files for usage example 8</h3>
<p><h3>File: x65923.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;X65923 X65923.1 H.sapiens fau mRNA
ttttttttttgactgaactaagtggcttttttattagagaaagccagaattacaaaagac
ttaagagttggcattggggcccttcttcttgccaaaggtgggcacaacgttgacaaagcg
ccggttgtactgcatccgccgcttagcccgacctgtcttcttcttcttcttctcctgttt
ggccaccttaggagtctgacctctcacttttccagcacgggccagggaaccatgaacttt
acctccaagcatgcggcctgctacttccagggtagtcagggcctccaccccgcactggcc
cagagtggcctcatcctccaggggcgcgcctgccaggagcacgacttgatcttccggggc
aatgccctccagtgaggctacatgagccttgatctgggcgaccgtttcctggccggtcac
ctcgaaggtgtgtagctcctgggcgcggacaaagagctgcatattggcgactgaacggcg
gtcccagctaccgcgaagatggagtcgagaaagaggaa
</pre>
</td></tr></table><p>

<a name="output.9"></a>
<h3>Output files for usage example 9</h3>
<p><h3>File: x65923.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;X65923 X65923.1 H.sapiens fau mRNA
tctttctcgactccatcttcg
</pre>
</td></tr></table><p>

<a name="output.10"></a>
<h3>Output files for usage example 10</h3>
<p><h3>File: x65923.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;X65923 X65923.1 H.sapiens fau mRNA
tctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcagct
ctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgccca
gatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcct
ggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgac
taccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggcccgtgc
tggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaagaagac
aggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgcccacctt
tggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttctcta
ataaaaaagccacttagttcagtcaaaaaa
</pre>
</td></tr></table><p>

<a name="output.11"></a>
<h3>Output files for usage example 11</h3>
<p><h3>File: hall.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;H45989 H45989.1 yo13c02.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA sequence.
ccggnaagctcancttggaccaccgactctcgantgnntcgccgcgggagccggntggan
aacctgagcgggactggnagaaggagcagagggaggcagcacccggcgtgacggnagtgt
gtggggcactcaggccttccgcagtgtcatctgccacacggaaggcacggccacgggcag
gggggtctatgatcttctgcatgcccagctggcatggccccacgtagagtggnntggcgt
ctcggtgctggtcagcgacacgttgtcctggctgggcaggtccagctcccggaggacctg
gggcttcagcttcccgtagcgctggctgcagtgacggatgctcttgcgctgccatttctg
ggtgctgtcactgtccttgctcactccaaaccagttcggcggtccccctgcggatggtct
gtgttgatggacgtttgggctttgcagcaccggccgccgagttcatggtngggtnaagag
atttgggttttttcn
</pre>
</td></tr></table><p>

<H2>
    Data files
</H2>


None.

<H2>
    Notes
</H2>

This description of what you can do when reading or writing files is not
specific to the program <b>seqret</b>.  All EMBOSS programs that read or write
sequences can do the same. 

<p>

<b>seqret</b> is often one of the first programs taught in EMBOSS training
courses.  This is because it is versatile, it is extremely powerful for
its size (17 lines of code) it illustrates many aspects of EMBOSS
programs and it was one of the first EMBOSS programs to be written, so
it has a special place in the hearts of EMBOSS developers. 

<p>

The name '<b>seqret</b>' derives both from its function ("sequence return") and
from the fact that immense amounts of functionality can come from so few
lines of source code - most of the work is done by the EMBOSS libraries
which the program calls and whose complexity is hidden, or "secret". 

<p>
The simplicity of the above description of this program greatly
understates the rich functionality of this program. 

<p>

Because EMBOSS programs can take a wide range of qualifiers that
slightly change the behaviour of the program when reading or writing a
sequence, this program can do many more things than simply "read and
write a sequence". 

<p>

<b>seqret</b> can read a sequence or many sequences from databases, files,
files of sequence names, the command-line or the output of other
programs and then can write them to files, the screen or pass them to
other programs.  Because it can read in a sequence from a database and
write it to a file, <b>seqret</b> is a program for extracting sequences from
databases.  Because it can write the sequence to the screen, <b>seqret</b> is a
program for displaying sequences. 

<p>

<b>seqret</b> can read sequences in any of a wide range of standard sequence
formats.  You can specify the input and output formats being used.  If
you don't specify the input format, <b>seqret</b> will try a set of possible
formats until it reads it in successfully.  Because you can specify the
output sequence format, <b>seqret</b> is a program to reformat a sequence. 

<p>

<b>seqret</b> can read in the reverse complement of a nucleic acid sequence. 
It therefore is a program for producing the reverse complement of a
sequence. 

<p>

<b>seqret</b> can read in a sequence whose begin and end positions you have
specified and write out that fragment.  It is therefore a utility for
doing simple extraction of a region of a sequence. 

<p>

<b>seqret</b> can change the case of the sequence being read in to upper or to
lower case.  It is therefore a simple sequence beautification utility. 

<p>

<b>seqret</b> can do any combination of the above functions.

<p>

The sequence input and output specification of this (and many other
EMBOSS programs) is described as being a Uniform Sequence Address. 

<p>

The Uniform Sequence Address, or USA, is a somewhat tongue-in-cheek
reference to a URL-style sequence naming used by all EMBOSS
applications. 

<p>

The USA is a very flexible way of specifying one or more sequences from
a variety of sources and includes sequence files, database queries and
external applications. 

<p>

See the full specification of USA syntax at:
<br>
<a href="http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html">
http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html
</a>

<p>

The basic USA syntax is one of: 

<ul>
<li>"file" 
<li>"file:entry" 
<li>"format::file" 
<li>"format::file:entry" 
<li>"database:entry" 
<li>"database"
<li>"@file" 
</ul>

<p>

Note that ':' separates the name of a file containing many possible
entries from the specific name of a sequence entry in that file.  It
also separates the name of a database from an entry in that database

<p>

Note also that '::' separates the specified format of a file from the
name of the file.  Normally the format can be omitted, in which case the
program will attempt to identify the correct format when reading the
sequence in and will default to using FASTA format when writing the
sequence out. 

<p>

Valid names of the databases set up in your local implementation of
EMBOSS can be seen by using the program '<a href="showdb.html">showdb</a>'.

<p>

Database queries, and individual entries in files that have more than
one sequence entry, use wildcards of "?" for any character and "*" for
any string of characters.  There are some problems with the Unix shell
catching these characters so they do need to be hidden in quotes or
preceded by a backslash on the Unix command line, (for example
"embl:hs\*")

<p>

The output USA name 'stdout' is special.  It makes the output go to the
device 'standard output'.  This is the screen, by default. 

<p>

<h3>Example USAs</h3>

The following are valid USAs for sequences:

<p>

<TABLE border=3>
<TR>
<TH>USA</TH>
<TH>Description</TH>
</TR>

<TR>
<TD>xxx.seq</TD>
<TD>A sequence file "xxx.seq" in any format</TD>
</TR>

<TR>
<TD>fasta::xxx.seq</TD>
<TD>A sequence file "xxx.seq" in fasta format</TD>
</TR>

<TR>
<TD>gcg::egmsmg.gcg</TD>
<TD>A sequence file "egmsmg.gcg" in GCG 9 format</TD>
</TR>

<TR>
<TD>egmsmg.gcg -sformat=gcg</TD>
<TD>A sequence file "egmsmg.gcg" in GCG 9 format</TD>
</TR>

<TR>
<TD>embl::x13776.em</TD>
<TD>A sequence file "x13776.em" in EMBL format</TD>
</TR>

<TR>
<TD>embl:x13776</TD>
<TD>EMBL entry X13776, using whatever access method is defined locally
for the EMBL database</TD>
</TR>

<TR>
<TD>embl:K01793</TD>
<TD>EMBL entry K01793, using whatever access method is defined locally
for the EMBL database and searching by accession number and entry name
(K01793 is a secondary accession number in this case for entry J01636)</TD>
</TR>

<TR>
<TD>embl-acc:K01793</TD>
<TD>EMBL entry X13776, using whatever access method is defined locally
for the EMBL database and searching by accession number only
</TD>
</TR>

<TR>
<TD>embl-id:x13776</TD>
<TD>EMBL entry x13776, using whatever access method is defined locally
for the EMBL database, and searching by ID only</TD>
</TR>

<TR>
<TD>embl:v0029*</TD>
<TD>EMBL entries V00290, V00291, and so on, usually in alphabetical order,
using whatever access method is defined locally for the EMBL database</TD>
</TR>

<TR>
<TD>embl or EMBL:*</TD>
<TD>All sequences in the EMBL database</TD>
</TR>

<TR>
<TD>@mylist</TD>
<TD>Reads file <i>mylist</i> and uses each line as a separate USA.  This
is standard VMS list file syntax, also used in SRS 4.0 but missing in
SRS 5.0 onwards.  The list file is a list of USAs (one per line).  List files
can contain references to other lists files or any other standard
USA.</TD>
</TR>

<TR>
<TD>list::mylist</TD>
<TD>Same as "@mylist" above</TD>
</TR>

<TR>
<TD>'getz -e [embl-id:x13776] |'</TD>
<TD>The pipe character "|" causes EMBOSS to fire up getz (SRS)
to extract entry x13776 from EMBL in EMBL format. Any application or
script which writes one or more sequences to stdout can be used in
this way.
</TR>

<TR>
<TD>asis::atacgcagttatctgaccat</TD>
<TD>So far the shortest USA we
could invent. In 'asis' format the name is the sequence so no file
needs to be opened. This is a special case.  It was intended as a
joke, but has proved quite useful for generating command lines when testing.</TD>
</TR>

</TABLE>

<h3>Input sequence formats</h3>

<p>

The input is a standard EMBOSS sequence query (also known as a 'USA').

<p>
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl

<p>

Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.

<p>
The input format can be specified by using the
command-line qualifier <tt>-sformat xxx</tt>, where 'xxx' is replaced
by the name of the required format.  The available format names are:
gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
(nbrf), swissprot (swiss, sw), dasgff and debug.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.


<h3>Output sequence formats</h3>

<p>

The output is a standard EMBOSS sequence file. 

<p>

The results can be output in one of several styles by using the
command-line qualifier <tt>-osformat xxx</tt>, where 'xxx' is replaced by
the name of the required format.  The available format names are: embl,
genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel,
feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.

<p>


<h3>Future directions</h3>

More formats, both for input and for output, can be easily added, so
suggestions are always welcome. 



<h3>Associated qualifiers</h3>

<p>

As noted previously there are many 'associated' qualifiers that alter
the behaviour of <b>seqret</b> when it reads in or writes out a sequence.  As
these are used in all EMBOSS programs that read in or write out
sequences, they are not reported by the '-help' qualifier.  They are
however reported by the pair of qualifiers: '-help -verbose':


<p>

Some of the more useful associated qualifiers are:

<table border=3>
<tr><th>Qualifier</th>		<th>Description</th></tr>

<tr><td>-sbegin</td><td>The first position to be used in the sequence</td></tr>
<tr><td>-send</td><td>The last position to be used in the sequence</td></tr>
<tr><td>-sreverse</td><td>Use the reverse complement of a nucleic acid sequence</td></tr>
<tr><td>-sask</td><td>Ask the user for begin/end/reverse information</td></tr>
<tr><td>-slower</td><td>Convert the sequence to lower case</td></tr>
<tr><td>-supper</td><td>Convert the sequence to upper case</td></tr>
<tr><td>-sformat</td><td>Specify the input sequence format</td></tr>
<tr><td>-osformat</td><td>Specify the output sequence format</td></tr>
<tr><td>-ossingle</td><td>Write each entry into a separate file</td></tr>
</table>

<p>

The set of associated qualifiers for sequences behave in different ways
depending on where they appear. 

<p>

If these qualifiers immediately follow a parameter they apply only to
that parameter and not to all cases.  If they occur before any
parameters, they apply to all following sequence parameters. 

<p>

If there are no two parameters of equal type, the order of parameters
and their qualifiers is irrelevant. 

<p>

Where a qualifier is defined more than once, for example "-sformat" for
2 input sequences to be aligned, the qualifier name can have a number to
indicate which sequence is meant.  "-sbegin2=25" will apply only to the
second sequence, no matter where it appears on the command line. 

<p>

The -sbegin and -send qualifiers take an integer number specifying the
position to begin or end reading a sequence.  If the number is positive,
the number is the position counting from the first base or residue of
the sequence.  If the number is negative the position is counted from
the end of the sequence, so position -1 is the last base or residue of
the sequence.  (If -sbegin 0 is used, it is assumed to be the same as
-sbegin 1 and -send 0 is the same as -send -1.)

<p>

The filter qualifier makes the program behave like a filter, reading its
(first) input 'file' from the standard input, and writing its (first)
output 'file' to the standard output.  The -filter qualifier will also
invoke the -auto qualifier, so the user is never prompted for any
missing values. 

<p>

Example:

<pre>

% cat sequence.seq | seqret -filter | lpr

</pre>

<p>

The example shows the application <b>seqret</b> being run with the -filter
qualifier.  The input file is 'piped' into the program using the unix
command cat and the output is 'piped' directly to the unix program lpr,
which will print it on the printer. 

<p>

When the -options qualifier is used and not all the parameters are given
on the command line, it will query the user for those parameters.  It
will not only query the user for the required parameters as it would do
without the -options qualifier, but it will also query the user for the
optional parameters.

<p>

When the -stdout qualifier is used, the user will still be prompted for
all the info that is required, but will write to standard output by
default.  The user will also still be prompted for an output filename,
in case the user wants to save the output to a file. 







<H2>
    References
</H2>

None.

<H2>
    Warnings
</H2>


None.

<H2>
    Diagnostic Error Messages
</H2>

None.


<H2>
    Exit status
</H2>

It always exits with a status of 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="aligncopy.html">aligncopy</a></td>
<td>Read and write alignments</td>
</tr>

<tr>
<td><a href="aligncopypair.html">aligncopypair</a></td>
<td>Read and write pairs from alignments</td>
</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>Copy and reformat a codon usage table</td>
</tr>

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

<tr>
<td><a href="degapseq.html">degapseq</a></td>
<td>Remove non-alphabetic (e.g. 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>Retrieve sequence entries from flatfile databases and files</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 sequence(s)</td>
</tr>

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

<tr>
<td><a href="featcopy.html">featcopy</a></td>
<td>Read and write a feature table</td>
</tr>

<tr>
<td><a href="featmerge.html">featmerge</a></td>
<td>Merge two overlapping feature tables</td>
</tr>

<tr>
<td><a href="featreport.html">featreport</a></td>
<td>Read and write a feature table</td>
</tr>

<tr>
<td><a href="feattext.html">feattext</a></td>
<td>Return a feature table original text</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>Create random nucleotide sequences</td>
</tr>

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

<tr>
<td><a href="maskambignuc.html">maskambignuc</a></td>
<td>Mask all ambiguity characters in nucleotide sequences with N</td>
</tr>

<tr>
<td><a href="maskambigprot.html">maskambigprot</a></td>
<td>Mask all ambiguity characters in protein sequences with X</td>
</tr>

<tr>
<td><a href="maskfeat.html">maskfeat</a></td>
<td>Write a sequence with masked features</td>
</tr>

<tr>
<td><a href="maskseq.html">maskseq</a></td>
<td>Write a sequence with masked regions</td>
</tr>

<tr>
<td><a href="newseq.html">newseq</a></td>
<td>Create a sequence file from a typed-in sequence</td>
</tr>

<tr>
<td><a href="nohtml.html">nohtml</a></td>
<td>Remove mark-up (e.g. HTML tags) from an ASCII text file</td>
</tr>

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

<tr>
<td><a href="nospace.html">nospace</a></td>
<td>Remove whitespace from an ASCII text file</td>
</tr>

<tr>
<td><a href="notab.html">notab</a></td>
<td>Replace tabs with spaces in an ASCII text file</td>
</tr>

<tr>
<td><a href="notseq.html">notseq</a></td>
<td>Write to file a subset of an input stream of sequences</td>
</tr>

<tr>
<td><a href="nthseq.html">nthseq</a></td>
<td>Write to file a single sequence from an input stream of sequences</td>
</tr>

<tr>
<td><a href="nthseqset.html">nthseqset</a></td>
<td>Read and write (return) one set of sequences from many</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 nucleotide sequence</td>
</tr>

<tr>
<td><a href="seqcount.html">seqcount</a></td>
<td>Read and count sequences</td>
</tr>

<tr>
<td><a href="seqretsetall.html">seqretsetall</a></td>
<td>Read and write (return) many sets of sequences</td>
</tr>

<tr>
<td><a href="seqretsplit.html">seqretsplit</a></td>
<td>Read sequences and write them to individual files</td>
</tr>

<tr>
<td><a href="sizeseq.html">sizeseq</a></td>
<td>Sort sequences by size</td>
</tr>

<tr>
<td><a href="skipredundant.html">skipredundant</a></td>
<td>Remove redundant sequences from an input set</td>
</tr>

<tr>
<td><a href="skipseq.html">skipseq</a></td>
<td>Read and write (return) sequences, skipping first few</td>
</tr>

<tr>
<td><a href="splitsource.html">splitsource</a></td>
<td>Split sequence(s) into original source sequences</td>
</tr>

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

<tr>
<td><a href="trimest.html">trimest</a></td>
<td>Remove poly-A tails from nucleotide sequences</td>
</tr>

<tr>
<td><a href="trimseq.html">trimseq</a></td>
<td>Remove unwanted characters from start and end of sequence(s)</td>
</tr>

<tr>
<td><a href="trimspace.html">trimspace</a></td>
<td>Remove extra whitespace from an ASCII text file</td>
</tr>

<tr>
<td><a href="union.html">union</a></td>
<td>Concatenate multiple sequences into a single sequence</td>
</tr>

<tr>
<td><a href="vectorstrip.html">vectorstrip</a></td>
<td>Remove vectors from the ends of nucleotide sequence(s)</td>
</tr>

<tr>
<td><a href="yank.html">yank</a></td>
<td>Add a sequence reference (a full USA) to a list file</td>
</tr>

</table>
<p>

Valid names of the databases set up in your local implementation of
EMBOSS can be seen by using the program 'showdb'. 


<H2>
    Author(s)
</H2>
Peter Rice
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.

<H2>
    History
</H2>

1999 - Written by Peter Rice
<br>
Feb 2002 - '-feature' qualifier added by Peter Rice

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


<H2>
    Comments
</H2>

<h3>Fasta output format</h3>

<h4>Question</h4>
When i tried to convert the EMBL format file into fasta format using the
program "<b>seqret</b>", I found that the Access.no appears twice... 

<p>

<pre>
&gt;AF102796 AF102796 Homo sapiens alphaE-catenin (CTNNA1) gene, exon 11.
</pre>
<p>

<h4>Answer</h4>

"It is not a bug ... it is a feature"
<p>


There are many "FASTA formats". EMBOSS uses the format that ACEDB and the
EBI genome projects use. The first field after the ID is the
accession number, so that accession numbers can be kept when sequences are
converted to FASTA format, without using the NCBI format (with '|'
characters in the IDs).
<p>

Your EMBL format file has IDs that look like accession numbers, so
EMBOSS fills in the accession number for each sequence, and reports it
in the FASTA format. 




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