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<HTML>
<HEAD>
<TITLE>
EMBOSS: stssearch
</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">
stssearch
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Search a DNA database for matches with a set of STS primers
<H2>
Description
</H2>
<b>stssearch</b> searches a DNA sequence database with a set of STS
primers and reports expected matches.
<p>
<b>stssearch</b>s reads in one or more sequences to be searched. For
each pair of primers, it looks for matches between a the primers
and the query sequence in either orientation.
<p>
Any matches found will be reported. Only one primer need match for it
to be reported..
<H2>
Usage
</H2>
<b>Here is a sample session with stssearch</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>stssearch </b>
Search a DNA database for matches with a set of STS primers
Input nucleotide sequence(s): <b>@eclac.list</b>
Primer pairs file: <b>lac.primers</b>
Output file [j01636.stssearch]: <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>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers:
[-seqall] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
[-infile] infile Primer pairs file
[-outfile] outfile [*.stssearch] Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-seqall" 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
-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
"-outfile" associated qualifiers
-odirectory3 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>[-seqall]<br>(Parameter 1)</td>
<td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-infile]<br>(Parameter 2)</td>
<td>Primer pairs file</td>
<td>Input file</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 3)</td>
<td>Output file name</td>
<td>Output file</td>
<td><i><*></i>.stssearch</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>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: eclac.list</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
#Formerly ECLAC
tembl:J01636
#Formerly ECLACA
tembl:X51872
#Formerly ECLACI
tembl:V00294
#Formerly ECLACY
tembl:V00295
#Formerly ECLACZ
tembl:V00296
</pre>
</td></tr></table><p>
<p><h3>File: lac.primers</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
PrimA ACCAGACACCCATCAACAG TATTTATGCCAGCCAGCCAG
PrimB CGAAAGAATAAGAGCAGGCAAG GTAAGAGAAATAGACAGGCGG
PrimC CGTCAGTATCCCCGTTTACAG TATCGCCAAAATCACCGCC
PrimD AATACGCAAACCGCCTCTCC TTATCCGCTCACAATTCCACAC
PrimE AATACGCAAACCGCCTCTCC CACAACCCGCTCACAATTCCA
</pre>
</td></tr></table><p>
<p>
The primers file consists of three columns separated by tabs or spaces.
<p>
The first column is the name of the primer pair.
<br>
The second column is the sequence of the first primer.
<br>
The third column is the sequence of the second primer.
<H2>
Output file format
</H2>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: j01636.stssearch</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
J01636: PrimA PrimerA matched at 532
J01636: (rev) PrimA PrimerB matched at 689
J01636: PrimB PrimerA matched at 5743
J01636: (rev) PrimB PrimerB matched at 5942
J01636: PrimC PrimerA matched at 2954
J01636: (rev) PrimC PrimerB matched at 3069
J01636: PrimD PrimerA matched at 1074
J01636: (rev) PrimD PrimerB matched at 1261
J01636: PrimE PrimerA matched at 1074
X51872: PrimB PrimerA matched at 98
X51872: (rev) PrimB PrimerB matched at 297
V00294: PrimA PrimerA matched at 484
V00294: (rev) PrimA PrimerB matched at 641
V00294: PrimD PrimerA matched at 1026
V00294: PrimE PrimerA matched at 1026
V00295: PrimB PrimerA matched at 1439
V00296: PrimC PrimerA matched at 1668
V00296: (rev) PrimC PrimerB matched at 1783
</pre>
</td></tr></table><p>
<p>
The output file consists of one line per match. This consists of:
<p>
<ul>
<li>The name of the sequence that the match is found in, followed by a ':'.
<li>If the match is in the reverse sense, it has a '(rev)'.
<li>The name of the primer pair.
<li>'PrimerA' or 'PrimerB'.
<li>'matched at' the start of the match position.
</ul>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
None.
<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="eprimer3.html">eprimer3</a></td>
<td>Picks PCR primers and hybridization oligos</td>
</tr>
<tr>
<td><a href="primersearch.html">primersearch</a></td>
<td>Searches DNA sequences for matches with primer pairs</td>
</tr>
</table>
<p>
If you want something that only reports matches of both primer pairs and
can find mismatches, use <A href="primersearch.html">primersearch</a>.
<H2>
Author(s)
</H2>
Peter Rice (pmr © ebi.ac.uk)
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
<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>
|
