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cmd_usearch_global.html
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cmd_usearch_global.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html lang="en">
<head>
<meta content="en-us" http-equiv="Content-Language"/>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type"/>
<meta content="no-cache, no-store, must-revalidate" http-equiv="Cache-Control"/>
<meta content="no-cache" http-equiv="Pragma"/>
<meta content="0" http-equiv="Expires"/>
<title>
allpairs_global command
</title>
<link href="stylesx.css" rel="stylesheet" type="text/css"/>
<style type="text/css">
body.c4 {background-color:#c0c0c0;}
div.c3 {position:absolute; top:45px; left:20px; width:830px; background-color:#ffffff; border-width:10px; border-style:solid;border-color:white;}
span.c2 {font-weight: bold}
div.c1 {position:absolute; top:10px; left:20px; width:850px; height:60px;}
.TopButtonPara { color:white; background-color:rgb(50,100,150); border-color:rgb(50,100,150); font-family:Arial, Helvetica, sans-serif; font-weight:normal; font-size:9pt; text-align:center; border-width:4px; border-style:solid; }
.TopButton { color:white; }
a.TopButton:link { text-decoration:none; }
a.TopButton:visited { text-decoration:none; }
a.TopButton:hover { color:orange; }
.NewButtonPara { color:white; background-color:rgb(50,100,150); border-color:rgb(50,100,150); font-family:Arial, Helvetica, sans-serif; font-weight:normal; font-size:9pt; text-align:center; border-width:4px; border-style:solid; }
.NewButton { color:white; }
a.NewButton:link { text-decoration:none; }
a.NewButton:visited { text-decoration:none; }
a.NewButton:hover { color:orange; }
.SideButtonPara { color:white; font-family:Arial, Helvetica, sans-serif; font-size:9pt; font-weight:normal; text-align:center; line-height:18px; }
.SideButton { color:white; }
a.SideButton:link { text-decoration:none; }
a.SideButton:visited { text-decoration:none; }
a.SideButton:hover { color:orange; }
</style>
</head>
<body style="background-color:#c0c0c0;">
<div>
<a href="https://drive5.com/usearch">
<img alt="USEARCH v12" src="usearch12_banner.jpg" style="position:absolute; top:40px; left:10px; padding:0px; border:0px;"/>
</a>
</div>
<div style="position:absolute; top:115px; left:10px; width:850px; background-color:#ffffff; min-height:500px">
<div style="position:relative; float:left; background-color:#696969; width:125px; left: 0px; min-height:500px; padding:5px; height: 125px;">
<div class="SideButtonPara" style="text-align:center; padding-top:5px;">
<a class="SideButton" href="index.html">
Docs home
</a>
<br/>
<hr style="border:0; border-bottom: 1px solid white;"/>
<a class="SideButton" href="cmds.html">
Commands
</a>
<br/>
<a class="SideButton" href="topics.html">
Topics
</a>
<br/>
<a class="SideButton" href="citation.html">
Publications
</a>
<br/>
</div>
</div>
<div class="ManText" style="left:20px; position: absolute; left:135px; width:695px; background-color:white; padding:10px">
<h1>
usearch_global command
</h1>
<span class="ManText">
Search for one (default) or a few high-identity hits to a database using the
<a href="usearch_algo.html">
USEARCH algorithm
</a>
. Alignments are global. To get more than one hit, increase -maxaccepts (see
<a href="accept_options.html">
accept options
</a>
).
</span>
<p>
<span class="ManText">
An identity threshold must be specified using the -
<a href="opt_id.html">
id option
</a>
. If full-length, exact matches are required, then it is better to use
<a href="DELETE_URL">
search_exact
</a>
than usearch_global with -id 1.0.
</span>
</p>
<p>
<span class="ManText">
The query file may be in
<a href="fasta_files.html">
FASTA
</a>
or
<a href="fastq_files.html">
FASTQ
</a>
format.
</span>
</p>
<p>
<span class="ManText">
A
<a href="db_files.html">
database file
</a>
must be specified using the -db option.
<a href="fasta_files.html">
FASTA
</a>
and .
<a href="udb_files.html">
udb
</a>
formats are supported. For large databases, .udb format is recommended (see
<a href="cmd_makeudb_usearch.html">
makeudb_usearch
</a>
command).
</span>
</p>
<p>
<span class="ManText">
The -
<a href="opt_strand.html">
strand
</a>
option is required for nucleotide databases.
</span>
</p>
<p>
<span class="ManText">
Nucleotide, protein and
<a href="translated_search.html">
translated searches
</a>
are supported.
</span>
</p>
<p>
<span class="ManText">
<b>
See also
</b>
<br/>
<a href="output_files.html">
Output files
</a>
<br/>
</span>
<span class="ManText">
<a href="accept_options.html">
Accept options
</a>
<br/>
<a href="DELETE_URL">
Weak hits
</a>
<br/>
<a href="termination_options.html">
Termination options
</a>
<br/>
<a href="indexing_options.html">
Indexing options
</a>
<br/>
<a href="multithreading.html">
Multithreading
</a>
<br/>
<a href="masking_options.html">
Masking options
</a>
<br/>
<a href="aln_params.html">
Alignment parameters
</a>
<br/>
<a href="aln_heuristics.html">
Alignment heuristics
</a>
</span>
</p>
<p>
<span class="ManText c3">
Examples
</span>
</p>
<p>
<span class="ManCode">
usearch -usearch_global query.fasta -db proteins.udb -id 0.8 -alnout hits.aln
<br/>
<br/>
usearch -usearch_global reads.fastq -db ESTs.fasta -id 0.9 -blast6out hits.b6 \
<br/>
-strand plus -maxaccepts 8 -maxrejects 256
<br/>
</span>
</p>
</div>
</div>
</body>
</html>