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91 compbio.pipeline._jpred</FONT>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.pipeline._jpred.Jpred4</B>
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100 <DT><PRE>public class <B>Jpred4</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>
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104 jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db
105 <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
107 jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
110 [--alignment <clustalW alignment>] The alignment which to use for prediction
112 [--profile=<path to HMM profile>]
114 [--db <database>] Database to use for PSI-BLAST querying. Default: uniref90 (
115 /homes/www-jpred/databases/uniref90.filt) Please note that database must be
118 [--pred-nohits] Toggle allowing Jpred to make predictions even when there are
121 [--logLevel=(ERROR|INFO|DEBUG)] one of ERROR, INFO, DEBUG [--help]
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126 <DT><B>Author:</B></DT>
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142 <TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/Jpred4.html#Jpred4()">Jpred4</A></B>()</CODE>
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159 <CODE> void</CODE></FONT></TD>
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191 public <B>Jpred4</B>()</PRE>
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