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7 compbio.pipeline._jpred
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83 Package compbio.pipeline._jpred
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88 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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89 <B>Class Summary</B></FONT></TH>
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91 <TR BGCOLOR="white" CLASS="TableRowColor">
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92 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastBlastComparator.html" title="class in compbio.pipeline._jpred">BlastBlastComparator</A></B></TD>
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95 <TR BGCOLOR="white" CLASS="TableRowColor">
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96 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastHmmerComparator.html" title="class in compbio.pipeline._jpred">BlastHmmerComparator</A></B></TD>
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99 <TR BGCOLOR="white" CLASS="TableRowColor">
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100 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred">BlastParser</A></B></TD>
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103 <TR BGCOLOR="white" CLASS="TableRowColor">
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104 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.html" title="class in compbio.pipeline._jpred">Hit</A></B></TD>
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107 <TR BGCOLOR="white" CLASS="TableRowColor">
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108 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.EvalueComporator.html" title="class in compbio.pipeline._jpred">Hit.EvalueComporator</A></B></TD>
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112 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.NumberComporator.html" title="class in compbio.pipeline._jpred">Hit.NumberComporator</A></B></TD>
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115 <TR BGCOLOR="white" CLASS="TableRowColor">
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116 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred">JackHmmerHitParser</A></B></TD>
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117 <TD>Parser for the following files:</TD>
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119 <TR BGCOLOR="white" CLASS="TableRowColor">
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120 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A></B></TD>
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121 <TD>jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db
122 <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
124 jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
127 [--alignment <clustalW alignment>] The alignment which to use for prediction
129 [--profile=<path to HMM profile>]
131 [--db <database>] Database to use for PSI-BLAST querying.</TD>
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133 <TR BGCOLOR="white" CLASS="TableRowColor">
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134 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A></B></TD>
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138 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A></B></TD>
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