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masking_options.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}
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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>
<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>
Masking options
</h1>
<span class="ManText">
USEARCH provides several methods for
<a href="masking.html">
masking
</a>
. Query and database sequences can be masked independently using masking provided by an external program or one of the built-in masking algorithms.
</span>
<p>
<span class="ManText c2">
Masking options
</span>
</p>
<div align="left">
<table border="0" cellpadding="5" cellspacing="0" style="width: 60%" summary="Table">
<tr>
<td align="right" class="c3" style="width: 102px">
<span class="ManText c2">
Option
</span>
</td>
<td align="center" class="c3" style="width: 28px">
</td>
<td align="left" class="c4" width="395">
<span class="ManText">
Description
</span>
</td>
</tr>
<tr>
<td align="right" class="c5" style="width: 102px" valign="top">
<span class="ManText">
-qmask
<i>
method
</i>
</span>
</td>
<td align="center" class="c5" style="width: 28px" valign="top">
</td>
<td align="left" class="c5" valign="top" width="395">
<span class="ManText">
Masking method for the query file. Used for database searches and clustering.
</span>
</td>
</tr>
<tr>
<td align="right" class="c3" style="width: 102px" valign="top">
<span class="ManText">
-dbmask
<i>
method
</i>
</span>
</td>
<td align="center" class="c3" style="width: 28px" valign="top">
</td>
<td align="left" class="c3" valign="top" width="395">
<span class="ManText">
Masking method for the
<a href="db_files.html">
database
</a>
. Used for
<a href="cmd_makeudb_usearch.html">
makeudb_usearch
</a>
and
<a href="DELETE_URL">
makeudb_ublast
</a>
and when a database is loaded from a FASTA file. Ignored if the database is a UDB file; the desired masking must be applied when the UDB file is created.
</span>
</td>
</tr>
<tr>
<td align="right" class="c5" style="width: 102px" valign="top">
<span class="ManText">
-
<a href="opt_hardmask.html">
hardmask
</a>
</span>
</td>
<td align="center" class="c5" style="width: 28px" valign="top">
</td>
<td align="left" class="c5" valign="top" width="395">
<span class="ManText">
Use hard masking (overwrite with N or X). Default is soft masking (upper case is unmasked, lower case is masked)..
</span>
</td>
</tr>
</table>
<p align="left">
<span class="ManText c2">
Masking methods
</span>
</p>
<table border="0" cellpadding="5" cellspacing="0" style="width: 60%" summary="Table">
<tr>
<td align="right" class="c3" style="width: 72px">
<span class="ManText c2">
Method
</span>
</td>
<td align="center" class="c4" style="width: 108px">
<span class="ManText">
Type
</span>
</td>
<td align="left" class="c4" width="338">
<span class="ManText">
Description
</span>
</td>
</tr>
<tr>
<td align="right" class="c5" style="width: 72px" valign="top">
<span class="ManText">
fastamino
</span>
</td>
<td align="center" class="c5" style="width: 108px" valign="top">
<span class="ManText">
protein
</span>
</td>
<td align="left" class="c5" valign="top" width="338">
<span class="ManText">
Unpublished method. Default for proteins.
</span>
</td>
</tr>
<tr>
<td align="right" class="c3" style="width: 72px" valign="top">
<span class="ManText">
fastnucleo
</span>
</td>
<td align="center" class="c3" style="width: 108px" valign="top">
<span class="ManText">
nucleotide
</span>
</td>
<td align="left" class="c3" valign="top" width="338">
<span class="ManText">
Unpublished method. Default for nucleotides.
</span>
</td>
</tr>
<tr>
<td align="right" class="c5" style="width: 72px" valign="top">
<span class="ManText">
seg
</span>
</td>
<td align="center" class="c5" style="width: 108px" valign="top">
<span class="ManText">
protein
</span>
</td>
<td align="left" class="c5" valign="top" width="338">
<span class="ManText">
Seg algorithm as used in BLASTP.
</span>
</td>
</tr>
<tr>
<td align="right" class="c3" style="width: 72px" valign="top">
<span class="ManText">
dust
</span>
</td>
<td align="center" class="c3" style="width: 108px" valign="top">
<span class="ManText">
nucleotide
</span>
</td>
<td align="left" class="c3" valign="top" width="338">
<span class="ManText">
Dust algorithm as used in BLASTN.
</span>
</td>
</tr>
<tr>
<td align="right" class="c5" style="width: 72px" valign="top">
<span class="ManText">
none
</span>
</td>
<td align="center" class="c5" style="width: 108px" valign="top">
<span class="ManText">
both
</span>
</td>
<td align="left" class="c5" valign="top" width="338">
<span class="ManText">
No masking, treat lower case and upper case letters as equivalent. This can be used if the input file has already been hard-masked.
</span>
</td>
</tr>
<tr>
<td align="right" class="c3" style="width: 72px" valign="top">
<span class="ManText">
user
</span>
</td>
<td align="center" class="c3" style="width: 108px" valign="top">
<span class="ManText">
both
</span>
</td>
<td align="left" class="c3" valign="top" width="338">
<span class="ManText">
Assume the input file has already been soft-masked so that lower case letters are masked.
</span>
</td>
</tr>
</table>
</div>
</div>
</div>
</body>
</html>