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<HTML>
<HEAD>
<TITLE>
EMBOSS: newseq
</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">
newseq
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Type in a short new sequence
<H2>
Description
</H2>
This allows you to type a sequence into a file in a quick and
easy manner.
<p>
The length of the sequence you can type in is restricted to a
fairly short length (typically less than 255 characters). This
length restriction is not a property of the EMBOSS package, but of the
computer system you are using. This is because, as you type in
response to a prompt from this program, what you type is stored in the
computer operating system before being handed over to the program.
There is often a limit of less than 255 characters on the length of a
response that a computer system will allow you to give.
<p>
Despite this restriction, it is expected that this program will
be a useful and easy way of constructing new sequence files.
<p>
(You wouldn't want to type a long sequence in by hand, anyway,
would you?)
<H2>
Usage
</H2>
<b>Here is a sample session with newseq</b>
<p>
Type in a short sequence to the file 'mycc.pep' in SWISSPROT format:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>newseq </b>
Type in a short new sequence.
Name of the sequence: <b>cytoc</b>
Description of the sequence: <b>fragment of cytochrome c</b>
Type of sequence
N : Nucleic
P : Protein
Type of sequence [N]: <b>p</b>
Enter the sequence: <b>KKKEERADLIAY</b>
output sequence [outfile.fasta]: <b>swiss::mycc.pep</b>
</pre></td></tr></table><p>
<p>
<a href="#output.1">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:
[-name] string The name of of the sequence should be a
single word that you will use to identify
the sequence. It should have no (or few)
punctuation characters in it. (Any string is
accepted)
[-description] string Enter any description of the sequence that
you require. (Any string is accepted)
[-type] menu [N] Type of sequence (Values: N (Nucleic); P
(Protein))
[-sequence] string The sequence itself.
Because of the limitation of the operating
system, you will only be able to type in a
short sequence of (typically) 250
characters, or so.
The keyboard will beep at you when you have
reached this limit and you will not be able
to press the RETURN/ENTER key until you have
deleted a few characters. (Any string is
accepted)
[-outseq] seqout [<sequence>.<format>] Sequence filename and
optional format (output USA)
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-outseq" associated qualifiers
-osformat5 string Output seq format
-osextension5 string File name extension
-osname5 string Base file name
-osdirectory5 string Output directory
-osdbname5 string Database name to add
-ossingle5 boolean Separate file for each entry
-oufo5 string UFO features
-offormat5 string Features format
-ofname5 string Features file name
-ofdirectory5 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>[-name]<br>(Parameter 1)</td>
<td>The name of of the sequence should be a single word that you will use to identify the sequence. It should have no (or few) punctuation characters in it.</td>
<td>Any string is accepted</td>
<td><i>An empty string is accepted</i></td>
</tr>
<tr>
<td>[-description]<br>(Parameter 2)</td>
<td>Enter any description of the sequence that you require.</td>
<td>Any string is accepted</td>
<td><i>An empty string is accepted</i></td>
</tr>
<tr>
<td>[-type]<br>(Parameter 3)</td>
<td>Type of sequence</td>
<td><table><tr><td>N</td> <td><i>(Nucleic)</i></td></tr><tr><td>P</td> <td><i>(Protein)</i></td></tr></table></td>
<td>N</td>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 4)</td>
<td>The sequence itself.
Because of the limitation of the operating system, you will only be able to type in a short sequence of (typically) 250 characters, or so.
The keyboard will beep at you when you have reached this limit and you will not be able to press the RETURN/ENTER key until you have deleted a few characters.</td>
<td>Any string is accepted</td>
<td><i>An empty string is accepted</i></td>
</tr>
<tr>
<td>[-outseq]<br>(Parameter 5)</td>
<td>Sequence filename and optional format (output USA)</td>
<td>Writeable sequence</td>
<td><i><*></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>
<H2>
Output file format
</H2>
<b>newseq</b> writes a normal sequence file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: mycc.pep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
ID cytoc Unreviewed; 12 AA.
DE fragment of cytochrome c
SQ SEQUENCE 12 AA; 1464 MW; 6F142FA88DADC40B CRC64;
KKKEERADLI AY
//
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
The length of the sequence you can type in is restricted to a
fairly short length (typically less than 255 characters).
If your computer beeps at you, you will typically have to delete
the last character you typed and press the RETURN key.
<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="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 © rfcgr.mrc.ac.uk)
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
<H2>
History
</H2>
Written (1999) - Gary Williams
<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
</BODY>
</HTML>
|
