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<html>
<head>
<title>Functional coupling notes</title>
<link rel='stylesheet' title='Grey' href='css/Grey.css' type='text/css'>
</head>
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<a name="top" />

<div style="text-align: center">
<h1>Notes on Direct and Inferred Functional Coupling</h1>

<h2>Rob<br />8/7/06</h2>
</div>

<h2>Index</h2>
<ol>
<li><a href="#howtorun">How to run the programs to calculate IFC</a></li>
<li><a href="#CouplingData">In the directory CouplingData</a></li>
<li><a href="#AbstractFuncCoupling">In the directory AbstractFuncCoupling</a></li>
<li><a href="#BBHs">data from BBHs</a></li>
<li><a href="#Programs">The programs for calculating DFC/IFC</a></li>
<li><a href="#score_dfcs">Comparison of Direct Functional Coupling Statistics</a></li>
<li><a href="#score_ifcs">Comparison of <em>Indirect</em> Functional Coupling Statistics</a>
</ol>
<hr>





<a name="howtorun"><h2>How to run the programs to calculate IFC</h2></a>
<p style="text-align: right"><A href="#top">Return to the top</a></p>
<p>As far as I can tell there are two different ways to run these programs. 

<ol>
<li>The first is to do everything from scratch with a pipe something along the lines of this:</li>
<p><tt>fig pegs_of 83333.1 | tr \\, \\n | indirect_functional_coupling_mcauliffe > FIG/Data/AbstractFuncCoupling/IFC/Data/83333.1</tt></p>
<li>The second is to just re-run it using the already found functionally coupled lists, which will just overwrite the old score with the new score, with a method like this:</li>
<p><tt>score_ifcs_mcauliffe < FIG/Data/AbstractFuncCoupling/IFC/Data/83333.1 > FIG/Data/AbstractFuncCoupling/IFC/NewData/83333.1</tt></p>
</li>
</ol>


<a name="CouplingData"><h2>In the directory: /disks/space0/fig/FIGdisk.anno_v5/FIG/Data/CouplingData</h2></a>
<p style="text-align: right"><A href="#top">Return to the top</a></p>

<p>There is a directory and a file:<br />
<ul>
	<li>The directory PCHs contains one file per genome. Each file contains the following columns:<br />
	<ol start=0>
		<li>peg1</li>
		<li>peg2</li>
		<li>peg3</li>
		<li>peg4</li>
		<li>iden1-3</li>
		<li>iden2-4</li>
		<li>para3</li>
		<li>para4</li>
		<li>rep</li>
	</ol>
	
	<p />
	<li>Notes:</li>
	<ol type=a>
		<li>iden1-3 and iden2-4 are the percent identitys from the sims between peg1 and peg3 or peg2 and peg4 respectively.</li>
		<li>para3 and para4 are ???</li>
		<li>rep is true if this PCH is a "representative pair"</li>
	</ol>
	<p />
		
	<li>The file <tt>scores</tt> contains peg1 peg2 and score between them.<br />
	To be present in this file peg1 and peg2 must have a score >= 4.</li>
</ul>
</p>

<a name="AbstractFuncCoupling"><h2>In the directory: /disks/space0/fig/FIGdisk.anno_v5/FIG/Data/AbstractFuncCoupling</h2></a>
<p style="text-align: right"><A href="#top">Return to the top</a></p>
<p>There are three directories, each with a sole Data directory. Each Data directory contains a series of files, one per genome.</p>

<ul>
	<li><strong>DFC/Data &nbsp; Direct Functional Coupling Data</strong>
	<p />The data in here contains the following columns:</li>
	<ol start=0>
		<li>peg1</li>
		<li>peg2</li>
		<li>Score (a fraction, the result from the dfcs methods described below)</li>
		<li>(no known meaning -- always blank)</li>
		<li>(no known meaning -- always blank)</li>
		<li>(no known meaning -- always blank)</li>
		<li>Functional Coupling Score (an integer)</li>
	</ol>
	<p />
	<li><strong>Fusion/Data &nbsp; Gene Fusion Data</strong>
	<p />The data in here contains the following columns:</li>
	<ol start=0>
		<li>peg1</li>
		<li>peg2</li>
		<li>Score</li>
		<li>peg3</li>
	</ol>
	
	<p>In this case peg1 and peg2 are both similar to peg3 and peg1 and peg2 are adjacent.</p>
	<p />
	<li><strong>IFC/Data &nbsp; Indirect Functional Coupling Data</strong>
	<p />The data in here contains the following columns:</li>
	<ol start=0>
		<li>peg1</li>
		<li>peg2</li>
		<li>Score (a fraction, the result from the score_ifcs methods described below)</li>
		<li>peg3</li>
		<li>peg4</li>
		<li>E-value of peg1 - peg3</li>
		<li>Functional Coupling Score for peg3 and peg4 (an integer)</li>
		<li>E-value of peg2 - peg4</li>
	</ol>
</ul>

<a name="BBHs"><h2>Data from BBHs</h2></a>
<p style="text-align: right"><A href="#top">Return to the top</a></p>
 
<p>This data is used from the BBHs. The files in /disks/space0/fig/FIGdisk.anno_v5/FIG/Data/Global/BBHs contain four columns - peg1, peg2, E-value between them, and normalized bit-score (based on the length of the proteins). This data is also returned by FIG->bbhs(peg). The BBHs is used as the input in indirect functional coupling.</p>


<a name="Programs"><h2>Programs</h2></a>
<p style="text-align: right"><A href="#top">Return to the top</a></p>

<p>These programs all deal with DFC/IFC scores</p>

<ol type=a>
	<li>FigKernelScripts/score_dfcs.pl</li>
	<li>FigKernelScripts/score_dfcs_mcauliffe.pl</li>
	<p>Score the direct functional coupling using Ross's and Jon's method</p>
	
	<p>The input for both of these programs is the three-ple of peg1, peg2, and score separated by tabs stored in /disks/space0/fig/FIGdisk.anno_v5/FIG/Data/CouplingData/scores</p>
	
	<p>The incantation of this is <tt>score_dfcs_mcauliffe < scores > output.txt</tt></p>
	
	<p><strong>A comparison of Ross's method and Jon's method is available <a href="#score_dfcs">below</a></strong></p>
	
	<p />
	
	<li>FigKernelScripts/score_ifcs.pl</li>
	<li>FigKernelScripts/score_ifcs_mcauliffe.pl</li>
	<p>Score the <em>indirect</em> functional coupling using Ross's  and Jon's methods</p>
	
	<p>The input for both of these programs is the Indirect Functional Coupling data in /disks/space0/fig/FIGdisk.anno_v5/FIG/Data/AbstractFuncCoupling/IFC/Data.
	The score_ifcs_mcauliffe program also takes into account the tough call flag for the functional role of proteins 3 and 4.</p>
	
	<p>The incantation of this is <tt>score_ifcs_mcauliffe < scores > output.txt</tt></p>
	
	<p><strong>A comparison of Ross's method and Jon's method is available <a href="#score_ifcs">below</a></strong></p>
	
	<p />
	
	<li>FigKernelScripts/direct_functional_coupling.pl
	<p>Generate the list of scores found in /disks/space0/fig/FIGdisk.anno_v5/FIG/Data/CouplingData/scores. Input is a list of pegs, output is a three-ple</p>
	
	<li>FigKernelScripts/indirect_functional_coupling.pl</li>
	<li>FigKernelScripts/indirect_functional_coupling_mcauliffe.pl</li>
	<p>Generate the IFC/Data files using either Ross's or Jon's methods. The only thing that is different between these two is how the fc component of the score is handled. There is no change to how the bbh component of the score is handled. However, I suspect that this may only have a small impact on the results
	... . The input to these programs is a list of pegs (e.g. all the pegs in an organism, and the output is the list as described under "IFC/Data &nbsp; Indirect Functional Coupling Data" above.</p>
</ol>

<a name="score_dfcs" />
<div style="text-align: center">
<h2>Comparison of Direct Functional Coupling Statistics</h2>
</div>

<p style="text-align: right"><A href="#top">Return to the top</a></p>

<p>Direct Functional Coupling Test</p>
<p>Here is a test data set, with 20 pairs chosen somewhat randomly from /disks/space0/fig/FIGdisk.anno_v5/FIG/Data/CouplingData/scores on anno-1. The only criteria was that the scores were separated over a reasonable range</p>
<p>The data in this table is that data, just converted into a table for easy viewing</p>

<table border=1>
<tr><td>fig|100226.1.peg.5</td><td>fig|100226.1.peg.6</td><td>5</td></tr>
<tr><td>fig|100226.1.peg.117</td><td>fig|100226.1.peg.118</td><td>18</td></tr>
<tr><td>fig|100226.1.peg.107</td><td>fig|100226.1.peg.108</td><td>26</td></tr>
<tr><td>fig|100226.1.peg.108</td><td>fig|100226.1.peg.107</td><td>31</td></tr>
<tr><td>fig|100226.1.peg.166</td><td>fig|100226.1.peg.167</td><td>41</td></tr>
<tr><td>fig|100226.1.peg.448</td><td>fig|100226.1.peg.449</td><td>57</td></tr>
<tr><td>fig|100226.1.peg.60</td><td>fig|100226.1.peg.61</td><td>64</td></tr>
<tr><td>fig|100226.1.peg.327</td><td>fig|100226.1.peg.328</td><td>75</td></tr>
<tr><td>fig|100226.1.peg.396</td><td>fig|100226.1.peg.395</td><td>81</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.249</td><td>92</td></tr>
<tr><td>fig|100226.1.peg.269</td><td>fig|100226.1.peg.268</td><td>100</td></tr>
<tr><td>fig|100226.1.peg.917</td><td>fig|100226.1.peg.918</td><td>117</td></tr>
<tr><td>fig|100226.1.peg.510</td><td>fig|100226.1.peg.511</td><td>129</td></tr>
<tr><td>fig|100226.1.peg.965</td><td>fig|100226.1.peg.964</td><td>132</td></tr>
<tr><td>fig|100226.1.peg.2894</td><td>fig|100226.1.peg.2893</td><td>147</td></tr>
<tr><td>fig|100226.1.peg.415</td><td>fig|100226.1.peg.417</td><td>150</td></tr>
<tr><td>fig|103690.1.peg.841</td><td>fig|103690.1.peg.836</td><td>160</td></tr>
<tr><td>fig|110662.3.peg.471</td><td>fig|110662.3.peg.472</td><td>179</td></tr>
<tr><td>fig|107806.1.peg.237</td><td>fig|107806.1.peg.238</td><td>182</td></tr>
<tr><td>fig|110662.3.peg.161</td><td>fig|110662.3.peg.160</td><td>198</td></tr>
</table>


<p class="dark_grey">First, using Ross's data with this command: <tt>score_dfcs < test.dat  > out1.txt</tt> and again, the data has been converted into a table for easier viewing</p>

<table border=1>
<tr><td>fig|100226.1.peg.5</td><td>fig|100226.1.peg.6</td><td>0.14</td><td></td><td></td><td></td><td>5</td><td></td></tr>
<tr><td>fig|100226.1.peg.117</td><td>fig|100226.1.peg.118</td><td>0.369</td><td></td><td></td><td></td><td>18</td><td></td></tr>
<tr><td>fig|100226.1.peg.107</td><td>fig|100226.1.peg.108</td><td>0.532</td><td></td><td></td><td></td><td>26</td><td></td></tr>
<tr><td>fig|100226.1.peg.108</td><td>fig|100226.1.peg.107</td><td>0.532</td><td></td><td></td><td></td><td>31</td><td></td></tr>
<tr><td>fig|100226.1.peg.166</td><td>fig|100226.1.peg.167</td><td>0.532</td><td></td><td></td><td></td><td>41</td><td></td></tr>
<tr><td>fig|100226.1.peg.448</td><td>fig|100226.1.peg.449</td><td>0.626</td><td></td><td></td><td></td><td>57</td><td></td></tr>
<tr><td>fig|100226.1.peg.60</td><td>fig|100226.1.peg.61</td><td>0.626</td><td></td><td></td><td></td><td>64</td><td></td></tr>
<tr><td>fig|100226.1.peg.327</td><td>fig|100226.1.peg.328</td><td>0.626</td><td></td><td></td><td></td><td>75</td><td></td></tr>
<tr><td>fig|100226.1.peg.396</td><td>fig|100226.1.peg.395</td><td>0.626</td><td></td><td></td><td></td><td>81</td><td></td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.249</td><td>0.626</td><td></td><td></td><td></td><td>92</td><td></td></tr>
<tr><td>fig|100226.1.peg.269</td><td>fig|100226.1.peg.268</td><td>0.554</td><td></td><td></td><td></td><td>100</td><td></td></tr>
<tr><td>fig|100226.1.peg.917</td><td>fig|100226.1.peg.918</td><td>0.554</td><td></td><td></td><td></td><td>117</td><td></td></tr>
<tr><td>fig|100226.1.peg.510</td><td>fig|100226.1.peg.511</td><td>0.554</td><td></td><td></td><td></td><td>129</td><td></td></tr>
<tr><td>fig|100226.1.peg.965</td><td>fig|100226.1.peg.964</td><td>0.554</td><td></td><td></td><td></td><td>132</td><td></td></tr>
<tr><td>fig|100226.1.peg.2894</td><td>fig|100226.1.peg.2893</td><td>0.554</td><td></td><td></td><td></td><td>147</td><td></td></tr>
<tr><td>fig|100226.1.peg.415</td><td>fig|100226.1.peg.417</td><td>0.554</td><td></td><td></td><td></td><td>150</td><td></td></tr>
<tr><td>fig|103690.1.peg.841</td><td>fig|103690.1.peg.836</td><td>0.554</td><td></td><td></td><td></td><td>160</td><td></td></tr>
<tr><td>fig|110662.3.peg.471</td><td>fig|110662.3.peg.472</td><td>0.554</td><td></td><td></td><td></td><td>179</td><td></td></tr>
<tr><td>fig|107806.1.peg.237</td><td>fig|107806.1.peg.238</td><td>0.554</td><td></td><td></td><td></td><td>182</td><td></td></tr>
<tr><td>fig|110662.3.peg.161</td><td>fig|110662.3.peg.160</td><td>0.554</td><td></td><td></td><td></td><td>198</td><td></td></tr>
</table>


<p class="dark_grey">Next , using Jon's method with this command: <tt>score_dfcs_mcauliffe < test.dat  > out1.txt</tt> and again, the data has been converted into a table for easier viewing</p>

<table border=1>
<tr><td>fig|100226.1.peg.5</td><td>fig|100226.1.peg.6</td><td>0.299120889411478</td><td></td><td></td><td></td><td>5</td><td></td></tr>
<tr><td>fig|100226.1.peg.117</td><td>fig|100226.1.peg.118</td><td>0.522949971399444</td><td></td><td></td><td></td><td>18</td><td></td></tr>
<tr><td>fig|100226.1.peg.107</td><td>fig|100226.1.peg.108</td><td>0.573657989539031</td><td></td><td></td><td></td><td>26</td><td></td></tr>
<tr><td>fig|100226.1.peg.108</td><td>fig|100226.1.peg.107</td><td>0.591405719793699</td><td></td><td></td><td></td><td>31</td><td></td></tr>
<tr><td>fig|100226.1.peg.166</td><td>fig|100226.1.peg.167</td><td>0.610144088896447</td><td></td><td></td><td></td><td>41</td><td></td></tr>
<tr><td>fig|100226.1.peg.448</td><td>fig|100226.1.peg.449</td><td>0.620123210113745</td><td></td><td></td><td></td><td>57</td><td></td></tr>
<tr><td>fig|100226.1.peg.60</td><td>fig|100226.1.peg.61</td><td>0.622282734197957</td><td></td><td></td><td></td><td>64</td><td></td></tr>
<tr><td>fig|100226.1.peg.327</td><td>fig|100226.1.peg.328</td><td>0.62631464430786</td><td></td><td></td><td></td><td>75</td><td></td></tr>
<tr><td>fig|100226.1.peg.396</td><td>fig|100226.1.peg.395</td><td>0.629459681793606</td><td></td><td></td><td></td><td>81</td><td></td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.249</td><td>0.637658534518548</td><td></td><td></td><td></td><td>92</td><td></td></tr>
<tr><td>fig|100226.1.peg.269</td><td>fig|100226.1.peg.268</td><td>0.645803565110239</td><td></td><td></td><td></td><td>100</td><td></td></tr>
<tr><td>fig|100226.1.peg.917</td><td>fig|100226.1.peg.918</td><td>0.669147037102104</td><td></td><td></td><td></td><td>117</td><td></td></tr>
<tr><td>fig|100226.1.peg.510</td><td>fig|100226.1.peg.511</td><td>0.689959339991436</td><td></td><td></td><td></td><td>129</td><td></td></tr>
<tr><td>fig|100226.1.peg.965</td><td>fig|100226.1.peg.964</td><td>0.695621589860686</td><td></td><td></td><td></td><td>132</td><td></td></tr>
<tr><td>fig|100226.1.peg.2894</td><td>fig|100226.1.peg.2893</td><td>0.725987893657268</td><td></td><td></td><td></td><td>147</td><td></td></tr>
<tr><td>fig|100226.1.peg.415</td><td>fig|100226.1.peg.417</td><td>0.732368037555034</td><td></td><td></td><td></td><td>150</td><td></td></tr>
<tr><td>fig|103690.1.peg.841</td><td>fig|103690.1.peg.836</td><td>0.754036525855967</td><td></td><td></td><td></td><td>160</td><td></td></tr>
<tr><td>fig|110662.3.peg.471</td><td>fig|110662.3.peg.472</td><td>0.7953658592143</td><td></td><td></td><td></td><td>179</td><td></td></tr>
<tr><td>fig|107806.1.peg.237</td><td>fig|107806.1.peg.238</td><td>0.801743440039699</td><td></td><td></td><td></td><td>182</td><td></td></tr>
<tr><td>fig|110662.3.peg.161</td><td>fig|110662.3.peg.160</td><td>0.834346803405206</td><td></td><td></td><td></td><td>198</td><td></td></tr>
</table>


<a name="score_ifcs" />
<div style="text-align: center">
<h2>Comparison of <em>Indirect</em> Functional Coupling Statistics</h2>
</div>

<p style="text-align: right"><A href="#top">Return to the top</a></p>

<p><em>Indirect</em> Functional Coupling Test</p>
<p>Here is a test data set, with 20 pairs chosen somewhat randomly from /disks/space0/fig/FIGdisk.anno_v5/FIG/Data/AbstractFuncCoupling/IFC/Data/ on anno-1. The only criteria was that the scores were separated over a reasonable range</p>
<p>The data in this table is that data, just converted into a table for easy viewing</p>

<table border=1>
<tr><td>fig|100226.1.peg.38</td><td>fig|100226.1.peg.5702</td><td>0.10</td><td>fig|262316.1.peg.2851</td><td>fig|262316.1.peg.2857</td><td>2.3e-14</td><td>4</td><td>2.5e-46</td></tr>
<tr><td>fig|100226.1.peg.55</td><td>fig|100226.1.peg.5951</td><td>0.27</td><td>fig|246201.1.peg.43</td><td>fig|246201.1.peg.42</td><td>7.5e-96</td><td>13</td><td>2.0e-74</td></tr>
<tr><td>fig|100226.1.peg.108</td><td>fig|100226.1.peg.107</td><td>0.41</td><td>fig|203122.1.peg.326</td><td>fig|203122.1.peg.327</td><td>0.0</td><td>29</td><td>0.0</td></tr>
<tr><td>fig|100226.1.peg.60</td><td>fig|100226.1.peg.6963</td><td>0.37</td><td>fig|70601.1.peg.1190</td><td>fig|70601.1.peg.1189</td><td>7.5e-41</td><td>32</td><td>1.7e-18</td></tr>
<tr><td>fig|100226.1.peg.195</td><td>fig|100226.1.peg.4905</td><td>0.38</td><td>fig|615.1.peg.1153</td><td>fig|615.1.peg.1151</td><td>2e-163</td><td>45</td><td>2.6e-28</td></tr>
<tr><td>fig|100226.1.peg.117</td><td>fig|100226.1.peg.118</td><td>0.45</td><td>fig|171440.1.peg.1288</td><td>fig|171440.1.peg.1290</td><td>8e-116</td><td>51</td><td>7.7e-23</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.2623</td><td>0.44</td><td>fig|272562.1.peg.596</td><td>fig|272562.1.peg.598</td><td>1.2e-38</td><td>67</td><td>2.4e-20</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.1867</td><td>0.44</td><td>fig|296591.1.peg.2173</td><td>fig|296591.1.peg.2172</td><td>5.0e-41</td><td>78</td><td>2.1e-37</td></tr>
<tr><td>fig|100226.1.peg.60</td><td>fig|100226.1.peg.2942</td><td>0.44</td><td>fig|1148.1.peg.2848</td><td>fig|1148.1.peg.2849</td><td>3.4e-33</td><td>80</td><td>5.2e-68</td></tr>
<tr><td>fig|100226.1.peg.268</td><td>fig|100226.1.peg.269</td><td>0.47</td><td>fig|246196.1.peg.5132</td><td>fig|246196.1.peg.5133</td><td>2e-125</td><td>96</td><td>1e-105</td></tr>
<tr><td>fig|100226.1.peg.269</td><td>fig|100226.1.peg.268</td><td>0.47</td><td>fig|266940.1.peg.2977</td><td>fig|266940.1.peg.2978</td><td>1e-110</td><td>103</td><td>2e-116</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.7436</td><td>0.45</td><td>fig|266835.1.peg.2769</td><td>fig|266835.1.peg.2768</td><td>1.4e-47</td><td>115</td><td>5.4e-46</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.2906</td><td>0.45</td><td>fig|204722.1.peg.2409</td><td>fig|204722.1.peg.2410</td><td>7.7e-41</td><td>127</td><td>7.8e-44</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.511</td><td>0.45</td><td>fig|246201.1.peg.1747</td><td>fig|246201.1.peg.1748</td><td>2.2e-48</td><td>133</td><td>7.8e-45</td></tr>
<tr><td>fig|100226.1.peg.446</td><td>fig|100226.1.peg.2472</td><td>0.44</td><td>fig|103690.1.peg.3883</td><td>fig|103690.1.peg.3881</td><td>7.9e-33</td><td>145</td><td>1.2e-34</td></tr>
<tr><td>fig|100226.1.peg.510</td><td>fig|100226.1.peg.511</td><td>0.45</td><td>fig|246196.1.peg.506</td><td>fig|246196.1.peg.507</td><td>3.0e-74</td><td>152</td><td>8.1e-77</td></tr>
<tr><td>fig|100226.1.peg.1526</td><td>fig|100226.1.peg.1525</td><td>0.48</td><td>fig|227882.1.peg.6791</td><td>fig|227882.1.peg.6792</td><td>1e-178</td><td>160</td><td>1e-107</td></tr>
<tr><td>fig|100226.1.peg.3902</td><td>fig|100226.1.peg.3903</td><td>0.49</td><td>fig|227882.1.peg.4263</td><td>fig|227882.1.peg.4262</td><td>0.0</td><td>177</td><td>1e-168</td></tr>
<tr><td>fig|100226.1.peg.4096</td><td>fig|100226.1.peg.6752</td><td>0.44</td><td>fig|259564.1.peg.2164</td><td>fig|259564.1.peg.2163</td><td>9.1e-38</td><td>182</td><td>3.2e-37</td></tr>
<tr><td>fig|1148.1.peg.2368</td><td>fig|1148.1.peg.2370</td><td>0.46</td><td>fig|266117.1.peg.2186</td><td>fig|266117.1.peg.2185</td><td>1.4e-83</td><td>190</td><td>8.4e-57</td></tr>
</table>

<p class="dark_grey">First, using Ross's data with this command: <tt>score_ifcs < test.dat > out1.txt</tt> and again, the data has been converted into a table for easier viewing</p>

<table border=1>
<tr><td>fig|100226.1.peg.38</td><td>fig|100226.1.peg.5702</td><td>0.112</td><td>fig|262316.1.peg.2851</td><td>fig|262316.1.peg.2857</td><td>2.3e-14</td><td>4</td><td>2.5e-46</td></tr>
<tr><td>fig|100226.1.peg.55</td><td>fig|100226.1.peg.5951</td><td>0.268</td><td>fig|246201.1.peg.43</td><td>fig|246201.1.peg.42</td><td>7.5e-96</td><td>13</td><td>2.0e-74</td></tr>
<tr><td>fig|100226.1.peg.108</td><td>fig|100226.1.peg.107</td><td>0.406</td><td>fig|203122.1.peg.326</td><td>fig|203122.1.peg.327</td><td>0.0</td><td>29</td><td>0.0</td></tr>
<tr><td>fig|100226.1.peg.60</td><td>fig|100226.1.peg.6963</td><td>0.368</td><td>fig|70601.1.peg.1190</td><td>fig|70601.1.peg.1189</td><td>7.5e-41</td><td>32</td><td>1.7e-18</td></tr>
<tr><td>fig|100226.1.peg.195</td><td>fig|100226.1.peg.4905</td><td>0.441</td><td>fig|615.1.peg.1153</td><td>fig|615.1.peg.1151</td><td>2e-163</td><td>45</td><td>2.6e-28</td></tr>
<tr><td>fig|100226.1.peg.117</td><td>fig|100226.1.peg.118</td><td>0.138</td><td>fig|171440.1.peg.1288</td><td>fig|171440.1.peg.1290</td><td>8e-116</td><td>51</td><td>7.7e-23</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.2623</td><td>0.439</td><td>fig|272562.1.peg.596</td><td>fig|272562.1.peg.598</td><td>1.2e-38</td><td>67</td><td>2.4e-20</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.1867</td><td>0.444</td><td>fig|296591.1.peg.2173</td><td>fig|296591.1.peg.2172</td><td>5.0e-41</td><td>78</td><td>2.1e-37</td></tr>
<tr><td>fig|100226.1.peg.60</td><td>fig|100226.1.peg.2942</td><td>0.444</td><td>fig|1148.1.peg.2848</td><td>fig|1148.1.peg.2849</td><td>3.4e-33</td><td>80</td><td>5.2e-68</td></tr>
<tr><td>fig|100226.1.peg.268</td><td>fig|100226.1.peg.269</td><td>0.469</td><td>fig|246196.1.peg.5132</td><td>fig|246196.1.peg.5133</td><td>2e-125</td><td>96</td><td>1e-105</td></tr>
<tr><td>fig|100226.1.peg.269</td><td>fig|100226.1.peg.268</td><td>0.470</td><td>fig|266940.1.peg.2977</td><td>fig|266940.1.peg.2978</td><td>1e-110</td><td>103</td><td>2e-116</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.7436</td><td>0.450</td><td>fig|266835.1.peg.2769</td><td>fig|266835.1.peg.2768</td><td>1.4e-47</td><td>115</td><td>5.4e-46</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.2906</td><td>0.450</td><td>fig|204722.1.peg.2409</td><td>fig|204722.1.peg.2410</td><td>7.7e-41</td><td>127</td><td>7.8e-44</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.511</td><td>0.450</td><td>fig|246201.1.peg.1747</td><td>fig|246201.1.peg.1748</td><td>2.2e-48</td><td>133</td><td>7.8e-45</td></tr>
<tr><td>fig|100226.1.peg.446</td><td>fig|100226.1.peg.2472</td><td>0.440</td><td>fig|103690.1.peg.3883</td><td>fig|103690.1.peg.3881</td><td>7.9e-33</td><td>145</td><td>1.2e-34</td></tr>
<tr><td>fig|100226.1.peg.510</td><td>fig|100226.1.peg.511</td><td>0.450</td><td>fig|246196.1.peg.506</td><td>fig|246196.1.peg.507</td><td>3.0e-74</td><td>152</td><td>8.1e-77</td></tr>
<tr><td>fig|100226.1.peg.1526</td><td>fig|100226.1.peg.1525</td><td>0.506</td><td>fig|227882.1.peg.6791</td><td>fig|227882.1.peg.6792</td><td>1e-178</td><td>160</td><td>1e-107</td></tr>
<tr><td>fig|100226.1.peg.3902</td><td>fig|100226.1.peg.3903</td><td>0.549</td><td>fig|227882.1.peg.4263</td><td>fig|227882.1.peg.4262</td><td>0.0</td><td>177</td><td>1e-168</td></tr>
<tr><td>fig|100226.1.peg.4096</td><td>fig|100226.1.peg.6752</td><td>0.440</td><td>fig|259564.1.peg.2164</td><td>fig|259564.1.peg.2163</td><td>9.1e-38</td><td>182</td><td>3.2e-37</td></tr>
<tr><td>fig|1148.1.peg.2368</td><td>fig|1148.1.peg.2370</td><td>0.460</td><td>fig|266117.1.peg.2186</td><td>fig|266117.1.peg.2185</td><td>1.4e-83</td><td>190</td><td>8.4e-57</td></tr>
</table>


<p class="dark_grey">Next , using Jon's method with this command: <tt>score_ifcs_mcauliffe < test.dat  > out1.txt</tt> and again, the data has been converted into a table for easier viewing</p>

<table border=1>
<tr><td>fig|100226.1.peg.38</td><td>fig|100226.1.peg.5702</td><td>0.881</td><td>fig|262316.1.peg.2851</td><td>fig|262316.1.peg.2857</td><td>2.3e-14</td><td>4</td><td>2.5e-46</td></tr>
<tr><td>fig|100226.1.peg.55</td><td>fig|100226.1.peg.5951</td><td>0.828</td><td>fig|246201.1.peg.43</td><td>fig|246201.1.peg.42</td><td>7.5e-96</td><td>13</td><td>2.0e-74</td></tr>
<tr><td>fig|100226.1.peg.108</td><td>fig|100226.1.peg.107</td><td>0.884</td><td>fig|203122.1.peg.326</td><td>fig|203122.1.peg.327</td><td>0.0</td><td>29</td><td>0.0</td></tr>
<tr><td>fig|100226.1.peg.60</td><td>fig|100226.1.peg.6963</td><td>0.801</td><td>fig|70601.1.peg.1190</td><td>fig|70601.1.peg.1189</td><td>7.5e-41</td><td>32</td><td>1.7e-18</td></tr>
<tr><td>fig|100226.1.peg.195</td><td>fig|100226.1.peg.4905</td><td>0.960</td><td>fig|615.1.peg.1153</td><td>fig|615.1.peg.1151</td><td>2e-163</td><td>45</td><td>2.6e-28</td></tr>
<tr><td>fig|100226.1.peg.117</td><td>fig|100226.1.peg.118</td><td>0.248</td><td>fig|171440.1.peg.1288</td><td>fig|171440.1.peg.1290</td><td>8e-116</td><td>51</td><td>7.7e-23</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.2623</td><td>0.792</td><td>fig|272562.1.peg.596</td><td>fig|272562.1.peg.598</td><td>1.2e-38</td><td>67</td><td>2.4e-20</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.1867</td><td>0.801</td><td>fig|296591.1.peg.2173</td><td>fig|296591.1.peg.2172</td><td>5.0e-41</td><td>78</td><td>2.1e-37</td></tr>
<tr><td>fig|100226.1.peg.60</td><td>fig|100226.1.peg.2942</td><td>0.801</td><td>fig|1148.1.peg.2848</td><td>fig|1148.1.peg.2849</td><td>3.4e-33</td><td>80</td><td>5.2e-68</td></tr>
<tr><td>fig|100226.1.peg.268</td><td>fig|100226.1.peg.269</td><td>0.846</td><td>fig|246196.1.peg.5132</td><td>fig|246196.1.peg.5133</td><td>2e-125</td><td>96</td><td>1e-105</td></tr>
<tr><td>fig|100226.1.peg.269</td><td>fig|100226.1.peg.268</td><td>0.846</td><td>fig|266940.1.peg.2977</td><td>fig|266940.1.peg.2978</td><td>1e-110</td><td>103</td><td>2e-116</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.7436</td><td>0.810</td><td>fig|266835.1.peg.2769</td><td>fig|266835.1.peg.2768</td><td>1.4e-47</td><td>115</td><td>5.4e-46</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.2906</td><td>0.810</td><td>fig|204722.1.peg.2409</td><td>fig|204722.1.peg.2410</td><td>7.7e-41</td><td>127</td><td>7.8e-44</td></tr>
<tr><td>fig|100226.1.peg.248</td><td>fig|100226.1.peg.511</td><td>0.810</td><td>fig|246201.1.peg.1747</td><td>fig|246201.1.peg.1748</td><td>2.2e-48</td><td>133</td><td>7.8e-45</td></tr>
<tr><td>fig|100226.1.peg.446</td><td>fig|100226.1.peg.2472</td><td>0.792</td><td>fig|103690.1.peg.3883</td><td>fig|103690.1.peg.3881</td><td>7.9e-33</td><td>145</td><td>1.2e-34</td></tr>
<tr><td>fig|100226.1.peg.510</td><td>fig|100226.1.peg.511</td><td>0.810</td><td>fig|246196.1.peg.506</td><td>fig|246196.1.peg.507</td><td>3.0e-74</td><td>152</td><td>8.1e-77</td></tr>
<tr><td>fig|100226.1.peg.1526</td><td>fig|100226.1.peg.1525</td><td>0.912</td><td>fig|227882.1.peg.6791</td><td>fig|227882.1.peg.6792</td><td>1e-178</td><td>160</td><td>1e-107</td></tr>
<tr><td>fig|100226.1.peg.3902</td><td>fig|100226.1.peg.3903</td><td>0.990</td><td>fig|227882.1.peg.4263</td><td>fig|227882.1.peg.4262</td><td>0.0</td><td>177</td><td>1e-168</td></tr>
<tr><td>fig|100226.1.peg.4096</td><td>fig|100226.1.peg.6752</td><td>0.792</td><td>fig|259564.1.peg.2164</td><td>fig|259564.1.peg.2163</td><td>9.1e-38</td><td>182</td><td>3.2e-37</td></tr>
<tr><td>fig|1148.1.peg.2368</td><td>fig|1148.1.peg.2370</td><td>0.828</td><td>fig|266117.1.peg.2186</td><td>fig|266117.1.peg.2185</td><td>1.4e-83</td><td>190</td><td>8.4e-57</td></tr>
</table>

























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