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3  <html>  <html>
4  <head>  <head>
5          <title>SEED/PIR Help Information</title>          <title>SEED/PIR Help Information</title>
6  <style><!--          <link rel='stylesheet' title='help' href='css/help.css' type='text/css'>
   
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7  </head>  </head>
8  <body>  <body>
9  <h1>Help On SEED/PIR Comparisons</h1>  <h1>Help On SEED/PIR Comparisons</h1>
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32  <p>By default the list only shows the Fully annotated PIR superfamilies, and not the preliminary superfamilies. However, you can reverse this, and display only the preliminray superfamilies if desired. The correspondences in preliminary superfamilies may be less well developed. <span class="example"><input type="checkbox" name="preliminary" value="on" />Show only preliminary PIR superfamilies</span>  <p>By default the list only shows the Fully annotated PIR superfamilies, and not the preliminary superfamilies. However, you can reverse this, and display only the preliminray superfamilies if desired. The correspondences in preliminary superfamilies may be less well developed. <span class="example"><input type="checkbox" name="preliminary" value="on" />Show only preliminary PIR superfamilies</span>
33  </p>  </p>
34    
35  <p>The three choices are to update the view which will present the same page, but with the choices that you have selected here, to show the correspondence between PIR superfamily and the SEED, and to reset the list back to the original values. The correspondence is <a href="#correspondence">described below</a></p>  <p>You can limit the PIR superfamilies shown on the list by some text. The text is a case-insensitive match, and you can search for something like "glutamate" or a superfamily number like "729"</p>
36    
37    <p>The choices are to update the view which will present the same page, but with the choices that you have selected here, to show the correspondence between PIR superfamily and the SEED, and to reset the list back to the original values. The correspondence is <a href="#correspondence">described below</a></p>
38    
39  <a name="datatables"><h2>Generate Data Tables</h2></a>  <a name="datatables"><h2>Generate Data Tables</h2></a>
40    
# Line 253  Line 210 
210  <a name="updates"><h2>Update Data</h2></a>  <a name="updates"><h2>Update Data</h2></a>
211  <p>You can download new data from the PIR ftp site and install the data directly. This is a two step process. First, we check to see whether the new file is more current than the old one (there is no point updating otherwise, unless, of course, you have added new genomes). Second, we actually get the data.</p>  <p>You can download new data from the PIR ftp site and install the data directly. This is a two step process. First, we check to see whether the new file is more current than the old one (there is no point updating otherwise, unless, of course, you have added new genomes). Second, we actually get the data.</p>
212    
213  <p>Click on the <span class="example"><input type="submit" name="submit" value="Check for updates" /></span> button to see whether there are new updates. You will then see a page that looks something along these lines (of course, the times will be different!):</p>  <p>Click on the <input type="submit" name="submit" value="Check for updates" /> button to see whether there are new updates. You will then see a page that looks something along these lines (of course, the times will be different!):</p>
214    
215  <p>This example is for files that are all current.</p>  <p>This example is for files that are all current.</p>
216  <div class="example">  <div class="example">
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233    
234  </div>  </div>
235    
236  <p>Clicking on the "Update Data" or "Update Anyway" buttons will start the download and reinitiate the comparison of the SEED data with the PIR data. This starts a complete install of the PIR data which may take some time, so you will have to be patient! You can also use this to refresh or reinstall your data if you believe that the data is out of date (for example if you have added new genomes).</P>  <p>Clicking on the "Update Data" or "Update Anyway" buttons will start the download and reinitiate the comparison of the SEED data with the PIR data. The downloading and installation of the data is run in the background using the script 'load_pirsf'  because it takes a signficant amount of time and resources. You can monitor the progress in the <a href="/FIG/seed_ctl.cgi">SEED control panel</a>. While the data is being installed you should really not use the PIR superfamilies. Although they will show up they are being edited, added, and deleted, and are therefore unstable. Installation of the data should take about 10-15 minutes.</p>
237    
238    <p>Once the update is run, you will see the front page again, however there will be a message telling you that the update is complete.</p>
239    
240    
241  <p>Once the update is run, you will see the front page again, however there will be a message telling you that the update is complete</p>  <a name="spreadsheet"><h2>Subsystem Spreadsheets</h2></a>
242    
243    <p>The correspondence between PIR and SEED is highlighted in the spreadsheets. A sample of a few columns are shown below. <small>Note this table is for demonstration purposes only and the correspondence will likely change.</small>
244    
245    <div class="example">
246    <table border=1>
247    
248    <tr>
249                    <td><b>Genome ID</b></td>
250                    <td><b>Organism</b></td>
251                    <td><b>Variant Code</b></td>
252                    <td><b>cysB</b></td>
253                    <td><b>cysC</b></td>
254                    <td><b>cysD</b></td>
255                    <td><b>cysI</b></td>
256                    <td><b>cysJ</b></td>
257                    <td><b>cysN</b></td>
258                    <td><b>cysQ</b></td>
259                    <td><b>cysS</b></td>
260            </tr>
261            <tr>
262                    <td><input type="text" name="genome214092.1" value="214092.1" size="15" /></td>
263                    <td>Yersinia pestis CO92 [B]</td>
264                    <td><input type="text" name="vcode214092.1" value="0311" size="10" /></td>
265                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.2277&user=master:RobE>2277</a></td>
266                    <td bgcolor="#00FF80"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3343&user=master:RobE>3343</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000544">10</a>] </sup> </td>
267                    <td bgcolor="#C0C0C0"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3345&user=master:RobE>3345</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF002936">1</a>] </sup> </td>
268                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3349&user=master:RobE>3349</a></td>
269                    <td bgcolor="#C0FF00"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3350&user=master:RobE>3350</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000207">9</a>] </sup> </td>
270                    <td bgcolor="#FF40C0"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3344&user=master:RobE>3344</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF003010">2</a>] </sup> </td>
271                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3504&user=master:RobE>3504</a></td>
272                    <td bgcolor="#FF8040"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3079&user=master:RobE>3079</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF001536">3</a>] </sup> </td>
273            </tr>
274            <tr>
275                    <td><input type="text" name="genome223926.1" value="223926.1" size="15" /></td>
276                    <td>Vibrio parahaemolyticus RIMD 2210633 [B]</td>
277                    <td><input type="text" name="vcode223926.1" value="0200" size="10" /></td>
278                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.1101&user=master:RobE>1101</a></td>
279                    <td bgcolor="#00FF80"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.296&user=master:RobE>296</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000544">10</a>] </sup> </td>
280                    <td bgcolor="#C0C0C0"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.292&user=master:RobE>292</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF002936">1</a>] </sup> </td>
281                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.2721&user=master:RobE>2721</a></td>
282                    <td bgcolor="#C0FF00"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.2722&user=master:RobE>2722</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000207">9</a>] </sup> </td>
283                    <td bgcolor="#FF40C0"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.293&user=master:RobE>293</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF003010">2</a>] </sup> </td>
284                    <td bgcolor="#FFFFFF"></td>
285                    <td bgcolor="#FF8040"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.1150&user=master:RobE>1150</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF001536">3</a>] </sup> </td>
286            </tr>
287            <tr>
288                    <td><input type="text" name="genome198214.1" value="198214.1" size="15" /></td>
289                    <td>Shigella flexneri 2a str. 301 [B]</td>
290                    <td><input type="text" name="vcode198214.1" value="1311" size="10" /></td>
291                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.1222&user=master:RobE>1222</a></td>
292                    <td bgcolor="#00FF80"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.2595&user=master:RobE>2595</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000544">10</a>] </sup> </td>
293                    <td bgcolor="#C0C0C0"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.2597&user=master:RobE>2597</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF002936">1</a>] </sup> </td>
294                    <td bgcolor="#C08080"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.2601&user=master:RobE>2601</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000244">8</a>] </sup> </td>
295                    <td bgcolor="#C0FF00"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.2602&user=master:RobE>2602</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000207">9</a>] </sup> </td>
296                    <td bgcolor="#FF40C0"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.2596&user=master:RobE>2596</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF003010">2</a>] </sup> </td>
297                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.4023&user=master:RobE>4023</a></td>
298                    <td bgcolor="#FF8040"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.444&user=master:RobE>444</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF001536">3</a>] </sup> </td>
299            </tr>
300    
301            <tr>
302                    <td><input type="text" name="genome272558.1" value="272558.1" size="15" /></td>
303                    <td>Bacillus halodurans C-125 [B]</td>
304                    <td><input type="text" name="vcode272558.1" value="2200" size="10" /></td>
305                    <td bgcolor="#FFFFFF"></td>
306                    <td bgcolor="#00FF80"><a href=/FIG/protein.cgi?prot=fig|272558.1.peg.1489&user=master:RobE>1489</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000544">10</a>] </sup> </td>
307                    <td bgcolor="#FFFFFF"></td>
308                    <td bgcolor="#C08080"><a href=/FIG/protein.cgi?prot=fig|272558.1.peg.610&user=master:RobE>610</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000244">8</a>] </sup> </td>
309                    <td bgcolor="#C0FF00"><a href=/FIG/protein.cgi?prot=fig|272558.1.peg.609&user=master:RobE>609</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000207">9</a>] </sup> </td>
310                    <td bgcolor="#FFFFFF"></td>
311                    <td bgcolor="#FFFFFF"></td>
312                    <td bgcolor="#FFC040"><a href=/FIG/protein.cgi?prot=fig|272558.1.peg.111&user=master:RobE>111</a>, <a href=http://theseed.uchicago.edu/FIG/protein.cgi?prot=fig|272558.1.peg.112&user=master:RobE>112</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF005520">5</a>, <a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF001536">3</a>] </sup> </td>
313            </tr>
314    </table>
315    </div>
316    
317    <p>The columns of the table are colored based on the superfamilies that the proteins are in, and in theory each column should be the same color and complete throughout.
318    <br />
319    Note that the small numbers that are slightly superscripted <span class="example"><sup style="margin: 1px"> [<a href="/FIG/pir.cgi?&user=master:RobE&pirsf=PIRSF005520">5</a>] </SUP></span> are linked to the PIR <a href="#correspondence">correspondence</a> table so you can click through and see proteins missing from either side as described above.</p>
320    
321    <p>This example demonstrates this different aspects of the PIR/SEED interactions:</p>
322    <ul>
323    <li>Protein in SEED subsystem but not in a PIR superfamily.</li>
324    <br>cysB is a conserved family in SEED but there is no corresponding PIR superfamily for these yet</br>
325    <li>Protein in SEED subsystem and in PIR superfamily.</li>
326    <br>cysC and cysJ are consistent across both PIR superfamilies and SEED subsystems.</br>
327    <li>Proteins in a PIR superfamily but not in a SEED subsystem</li>
328    <br>You can't actually see these from this table, you have to look at the <a href="#correspondence">correspondence</a> table.</br>
329    <li>Proteins in SEED subsystem but missing from the PIR superfamily.</li>
330    <br>For example, cysI is missing from the superfamily for the first two organisms</br>
331    <li>Duplicate proteins</li>
332    <br>Some proteins like cysS either have two proteins in one cell or may have one protein mapping to two superfamilies. These are shown as more than one entry in the superscript</br>
333    </ul>
334    
335    
336    

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