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<HTML>
<HEAD>
<TITLE>
EMBOSS
</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">
primersearch
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Searches DNA sequences for matches with primer pairs
<H2>
Description
</H2>
<b>primersearch</b> reads in primer pairs from an input file and searches
them against sequence(s) specified by the user. Each of the primers in
a pair is searched against the sequence and potential amplimers are
reported.
<p>
The user can specify a maximum percent mismatch level; for example,
10% mismatch on a primer of length 20bp means that the program will
classify a primer as matching a sequence if 18 of the 20 base pairs
matches.
<p>
It will only report matches if both primers in the pair have a match in
opposite orientations.
<H2>
Usage
</H2>
<b>Here is a sample session with primersearch</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>primersearch tembl:z52466 </b>
Searches DNA sequences for matches with primer pairs
Primer pairs file: <b>primers</b>
Allowed percent mismatch [0]: <b></b>
Whitehead primer3_core program output file [z52466.primersearch]: <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>
Here we run the same example but allowing 20% mismatch between the primers and the sequence:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>primersearch tembl:z52466 </b>
Searches DNA sequences for matches with primer pairs
Primer pairs file: <b>primers</b>
Allowed percent mismatch [0]: <b>20</b>
Whitehead primer3_core program output file [z52466.primersearch]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#output.2">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
[-mismatchpercent] integer [0] Allowed percent mismatch (Any integer
value)
[-outfile] outfile [*.primersearch] Whitehead primer3_core
program output file
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
-odirectory4 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>[-mismatchpercent]<br>(Parameter 3)</td>
<td>Allowed percent mismatch</td>
<td>Any integer value</td>
<td>0</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 4)</td>
<td>Whitehead primer3_core program output file</td>
<td>Output file</td>
<td><i><*></i>.primersearch</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>primersearch</b> reads in any nucleic acid sequence USAs.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:z52466' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>File: primers</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
# This is my primer file
D1S243 cacacaggctcacatgcc gctccagcgtcatggact
D1S468 aattaaccgttttggtcct gcgacacacacttccc
D1S2845 ccaaagggtgcttctc gtggcattccaacctc
D1S1608 gatggcttttggggactatt cactgagccaagtgacacag
D1S2893 aaaacatcaactctcccctg ctcaaaccccaataagcctt
D1S2660 cacacatgcacatgcac agtgacaccagcaggg
</pre>
</td></tr></table><p>
<p><h3>Database entry: tembl:z52466</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID Z52466; SV 1; linear; genomic DNA; STS; HUM; 389 BP.
XX
AC Z52466;
XX
DT 18-MAR-1996 (Rel. 47, Created)
DT 09-SEP-2004 (Rel. 81, Last updated, Version 4)
XX
DE H.sapiens (D1S2660) DNA segment containing (CA) repeat; clone AFMa203yc1;
DE single read.
XX
KW CA repeat; dinucleotide repeat; GT repeat; microsatellite DNA;
KW microsatellite marker; repeat polymorphism; STS.
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 1-389
RA Weissenbach J.;
RT ;
RL Submitted (01-SEP-1995) to the EMBL/GenBank/DDBJ databases.
RL Genethon, B.P. 60, 91002 Evry Cedex France. E-mail:
RL Jean.Weissenbach@genethon.fr
XX
RN [2]
RP 1-389
RX DOI; 10.1038/380152a0.
RX PUBMED; 8600387.
RA Dib C., Faure S., Fizames C., Samson D., Drouot N., Vignal A.,
RA Millasseau P., Marc S., Hazan J., Seboun E., Lathrop M., Gyapay G.,
RA Morissette J., Weissenbach J.;
RT "A comprehensive genetic map of the human genome based on 5,264
RT microsatellites";
RL Nature 380(6570):152-154(1996).
XX
DR GDB; 606855.
XX
CC full automatic;
XX
FH Key Location/Qualifiers
FH
FT source 1..389
FT /organism="Homo sapiens"
FT /chromosome="1"
FT /mol_type="genomic DNA"
FT /clone_lib="genomic DNA"
FT /cell_line="CEPH 134702"
FT /note="cloning vector is M13mp18"
FT /db_xref="taxon:9606"
XX
SQ Sequence 389 BP; 118 A; 124 C; 86 G; 57 T; 4 other;
agctgtgtgc acacaacatg anggggcaca catgcacatg cacacatgcc cacatgcata 60
tgcacacaca cacacacaca cacacacaca ttcatgccca agcacgccca ccctcatgtc 120
tcaccatgtg cacataacac acagtcacat ataccctggc acacatgccc acatgcagac 180
acgaaacaca ggcccacgnt tncatgcaca caggtatggg cacacatacc atgcacacat 240
aangacaaat accaggccag acatgatttg cccctgctgg tgtcactgtt aagtgtgaca 300
gacaagcaga ggacacacac ccacctggga cgcggggctt caggagagag gcagacctaa 360
tagggcccgg attcggggct ggggaggct 389
//
</pre>
</td></tr></table><p>
<p>
The input primer file has the following format:
<p>
Comment lines start with a '#'
<br>
Lines with primer information have three fields separated by spaces or TAB characters. The columns contain:
<br>
<ol>
<li>The name of the primer pair - this is reported in the output.
<li>The sequence of the first primer.
<li>The sequence of the second primer.
</ol>
<p>
Empty files will cause primersearch to note that no primers have
been found, and to exit.
<H2>
Output file format
</H2>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: z52466.primersearch</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Primer name D1S243
Primer name D1S468
Primer name D1S2845
Primer name D1S1608
Primer name D1S2893
Primer name D1S2660
Amplimer 1
Sequence: Z52466 Z52466
H.sapiens (D1S2660) DNA segment containing (CA) repeat; clone AFMa203yc1; single read.
CACACATGCACATGCAC hits forward strand at 27 with 0 mismatches
AGTGACACCAGCAGGG hits reverse strand at [103] with 0 mismatches
Amplimer length: 261 bp
</pre>
</td></tr></table><p>
<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: z52466.primersearch</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Primer name D1S243
Primer name D1S468
Primer name D1S2845
Primer name D1S1608
Primer name D1S2893
Primer name D1S2660
Amplimer 1
Sequence: Z52466 Z52466
H.sapiens (D1S2660) DNA segment containing (CA) repeat; clone AFMa203yc1; single read.
CACACATGCACATGCAC hits forward strand at 49 with 2 mismatches
AGTGACACCAGCAGGG hits reverse strand at [103] with 0 mismatches
Amplimer length: 239 bp
Amplimer 2
Sequence: Z52466 Z52466
H.sapiens (D1S2660) DNA segment containing (CA) repeat; clone AFMa203yc1; single read.
CACACATGCACATGCAC hits forward strand at 27 with 0 mismatches
AGTGACACCAGCAGGG hits reverse strand at [103] with 0 mismatches
Amplimer length: 261 bp
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
Every potential amplimer will be reported; if one primer matches the
forward strand twice and the other matches the reverse strand only
once, two potential amplimers are reported. If the reverse primer
matches twice, four potential amplimers are reported.
<p>
Each primer pair consists of a name, followed by two primer sequences,
primerA and primerB. The program first compares primerA to the forward
strand and if it matches, primerB is compared to the reverse
strand. The approach is then reversed, with the primerB being compared
to the forward strand and primerA to the reverse. In this way all
possible amplimers are reported.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
This program is slow.
<br>
Don't try searching all of EMBL!
<br>
It might not be sensible to search all of the human section of EMBL -
in 2000, this would take a day to do with one primer pair.
<br>
It will take longer with more primer pairs.
<br>
It will take longer if you allow mismatches.
<H2>
Diagnostic Error Messages
</H2>
"No suitable primers found - exiting" means that either the primers
file was empty or there were no compilable primer pairs contained in it.
<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="eprimer3.html">eprimer3</a></td>
<td>Picks PCR primers and hybridization oligos</td>
</tr>
<tr>
<td><a href="stssearch.html">stssearch</a></td>
<td>Search a DNA database for matches with a set of STS primers</td>
</tr>
</table>
<p>
<a href="stssearch.html">stssearch</a> does something similar, but doesn't
allow you to find mismatches and will report any match in any
orientation and doesn't require you to have both primers matching.
<H2>
Author(s)
</H2>
Val Curwen (vac © sanger.ac.uk)
<br>
Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK.
<H2>
History
</H2>
Written Aug 2000 - Val Curwen
<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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