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cmd_search_16s.html
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cmd_search_16s.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"/>
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<meta content="no-cache, no-store, must-revalidate" http-equiv="Cache-Control"/>
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<title>
allpairs_global command
</title>
<link href="stylesx.css" rel="stylesheet" type="text/css"/>
<style type="text/css">
body.c4 {background-color:#c0c0c0;}
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</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>
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<a class="SideButton" href="index.html">
Docs home
</a>
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<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>
search_16s command (64-bit only)
</h1>
<strong>
<br/>
<a href="search_16s_algo.html">
<img alt="Image" class="auto-style1 c2" src="search_16s_graph_small.jpg"/>
</a>
See also
<br/>
</strong>
<a href="search_16s_algo.html">
SEARCH_16S algorithm
</a>
<br/>
<a href="citation.html">
SEARCH_16S paper
</a>
<br/>
<br/>
The search_16s command searches a long sequence such as a chromosome or contig for 16S genes.
<br/>
It has exceptionally high accuracy, finding at least 99.9% of known 16S genes with few or no false positives.
<br/>
<br/>
A bit vector database is required, specified by the -bitvec option. See
<a href="bitvec.html">
creating a bit vector file for the search_16s command
</a>
.
<br/>
<br/>
Input can be in FASTQ or FASTA format.
<br/>
<br/>
-hitsout option
<br/>
FASTA file containing "hits", i.e. regions with elevated density of signature words. These are candidate 16S genes with flanking sequence (see paper for details).
<br/>
<br/>
-fastaout option
<br/>
FASTA file containing predicted 16S genes.
<br/>
<br/>
-fragout option
<br/>
FASTA file containg probable fragments of 16S genes which lack one or both identifying motifs.
<br/>
<br/>
-tabbedout option
<br/>
Tabbed text file containg records for query sequences, hits, full-length genes and fragments.
<br/>
<br/>
-start_motif option
<br/>
Start motif. Default GNTTGATCNTGNC.
<br/>
<br/>
-end_motif option
<br/>
End motif. Default AGTCNNAACAAGGTANCNNTA.
<br/>
<br/>
-min_gene_length option
<br/>
Minimum gene length. Default 1200.
<br/>
<br/>
-max_gene_length option
<br/>
Maximum gene length. Default 2000.
<br/>
<br/>
-maxstartdiffs option
<br/>
Maximum number of mismatches with the start motif. Default 4.
<br/>
<br/>
-maxenddiffs option
<br/>
Maximum number of mismatches with the end motif. Default 4.
<br/>
<br/>
<strong>
Example
<br/>
<br/>
</strong>
<span class="ManCode">
usearch -search_16s contigs.fa -bitvec gg97.bitvec -fastaout 16s.fa -tabbedout results.txt
<br/>
</span>
</div>
</div>
</body>
</html>