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  83 Package compbio.pipeline._jpred\r
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  85 \r
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  88 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
  89 <B>Class Summary</B></FONT></TH>\r
  90 </TR>\r
  91 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  92 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastBlastComparator.html" title="class in compbio.pipeline._jpred">BlastBlastComparator</A></B></TD>\r
  93 <TD>&nbsp;</TD>\r
  94 </TR>\r
  95 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  96 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastHmmerComparator.html" title="class in compbio.pipeline._jpred">BlastHmmerComparator</A></B></TD>\r
  97 <TD>&nbsp;</TD>\r
  98 </TR>\r
  99 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 100 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred">BlastParser</A></B></TD>\r
 101 <TD>&nbsp;</TD>\r
 102 </TR>\r
 103 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 104 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.html" title="class in compbio.pipeline._jpred">Hit</A></B></TD>\r
 105 <TD>&nbsp;</TD>\r
 106 </TR>\r
 107 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 108 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.EvalueComporator.html" title="class in compbio.pipeline._jpred">Hit.EvalueComporator</A></B></TD>\r
 109 <TD>&nbsp;</TD>\r
 110 </TR>\r
 111 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 112 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.NumberComporator.html" title="class in compbio.pipeline._jpred">Hit.NumberComporator</A></B></TD>\r
 113 <TD>&nbsp;</TD>\r
 114 </TR>\r
 115 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 116 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred">JackHmmerHitParser</A></B></TD>\r
 117 <TD>Parser for the following files:</TD>\r
 118 </TR>\r
 119 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 120 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A></B></TD>\r
 121 <TD>jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db
 122  <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
 123
 124  jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
 125  want to predict OR
 126
 127  [--alignment <clustalW alignment>] The alignment which to use for prediction
 128
 129  [--profile=<path to HMM profile>]
 130
 131  [--db <database>] Database to use for PSI-BLAST querying.</TD>\r
 132 </TR>\r
 133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 134 <TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A></B></TD>\r
 135 <TD>&nbsp;</TD>\r
 136 </TR>\r
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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>\r
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