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7 Uses of Package compbio.runner.disorder
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84 <B>Uses of Package<br>compbio.runner.disorder</B></H2>
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90 Packages that use <A HREF="../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>
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94 <TD> </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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98 <TD> </TD>
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103 <A NAME="compbio.runner.disorder"><!-- --></A>
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104 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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106 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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107 Classes in <A HREF="../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A> used by <A HREF="../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>
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109 <TR BGCOLOR="white" CLASS="TableRowColor">
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110 <TD><B><A HREF="../../../compbio/runner/disorder/class-use/Disembl.html#compbio.runner.disorder"><B>Disembl</B></A></B>
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113 DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
114 fold_rem465 sequence_file print
116 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
118 This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
119 capable of outputting raw values
121 The values of the parameters are hard coded in DisEMBL.py script.</TD>
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123 <TR BGCOLOR="white" CLASS="TableRowColor">
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124 <TD><B><A HREF="../../../compbio/runner/disorder/class-use/GlobPlot.html#compbio.runner.disorder"><B>GlobPlot</B></A></B>
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127 ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
129 FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
130 Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
132 Hard-coded values are 10 15 74 4 5.</TD>
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134 <TR BGCOLOR="white" CLASS="TableRowColor">
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135 <TD><B><A HREF="../../../compbio/runner/disorder/class-use/IUPred.html#compbio.runner.disorder"><B>IUPred</B></A></B>
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138 iupred sequenceFile <short long glob >
140 Maximum sequence length is 40000 chars.</TD>
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142 <TR BGCOLOR="white" CLASS="TableRowColor">
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143 <TD><B><A HREF="../../../compbio/runner/disorder/class-use/Jronn.html#compbio.runner.disorder"><B>Jronn</B></A></B>
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146 Command line
148 java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</TD>
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153 <A NAME="compbio.ws.server"><!-- --></A>
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156 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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157 Classes in <A HREF="../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A> used by <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>
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159 <TR BGCOLOR="white" CLASS="TableRowColor">
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160 <TD><B><A HREF="../../../compbio/runner/disorder/class-use/Disembl.html#compbio.ws.server"><B>Disembl</B></A></B>
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163 DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
164 fold_rem465 sequence_file print
166 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
168 This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
169 capable of outputting raw values
171 The values of the parameters are hard coded in DisEMBL.py script.</TD>
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173 <TR BGCOLOR="white" CLASS="TableRowColor">
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174 <TD><B><A HREF="../../../compbio/runner/disorder/class-use/GlobPlot.html#compbio.ws.server"><B>GlobPlot</B></A></B>
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177 ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
179 FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
180 Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
182 Hard-coded values are 10 15 74 4 5.</TD>
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184 <TR BGCOLOR="white" CLASS="TableRowColor">
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185 <TD><B><A HREF="../../../compbio/runner/disorder/class-use/IUPred.html#compbio.ws.server"><B>IUPred</B></A></B>
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188 iupred sequenceFile <short long glob >
190 Maximum sequence length is 40000 chars.</TD>
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