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Wed Feb 7 00:28:34 2007 UTC (12 years, 8 months ago) by redwards
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CVS Tags: rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, rast_rel_2008_09_30, rast_rel_2010_0526, rast_rel_2014_0729, rast_rel_2009_05_18, rast_rel_2009_0925, rast_rel_2010_1206, rast_rel_2010_0118, rast_rel_2009_02_05, rast_rel_2011_0119, rast_rel_2008_12_18, rast_rel_2008_10_09, rast_release_2008_09_29, rast_rel_2008_04_23, rast_rel_2008_08_07, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, rast_rel_2008_10_29, rast_rel_2009_03_26, rast_rel_2008_11_24, HEAD
Changes since 1.7: +46 -0 lines
adding Ross help on making trees

<html><head><meta http-equiv="content-type" content="text/html; charset=UTF-8"><title>SEED Tips</title>

<link rel='stylesheet' title='help' href='css/help.css' type='text/css'>	

<h1>TIPS IN SEED</h1>

<a name="gene_names"><h2>Defining gene names</h2></a>

<li>Role1 @ Role2 </li>
<p>A monofunctional enzyme that can catalyze two different reactions, both role 1 or role 2</p>

<li>Role1 / Role2</li>

<p>A bifunctional enzyme that does two unrelated roles, role 1 and role 2</p>

<li>Role1 ; Role2</li>

<p>Does one of either role 1 or role 2 but we don't know which</p>


<a name="but_not"><H2>But Not</h2>

<p>There are several occasions where you are sure what something <i>is not</i> but you don't know what it <i>is</i>. For example, there is a protein in your spreadsheet that is a duplicate, and you are sure that it is the wrong one because it is not a cluster. To remove it, you can add "But Not" to the end of the annotation. This is very useful as you can see what things have been checked and shown not to be something!</p>

<a name="replace_names"><h2>Replace names.</h2></a>

<li>Suppose that you wish to rewrite all assignments of the form <span="code">homoserine kinase</code> with <span="code">Homoserine kinase (EC</span>.</li>
<p>To do this, you first go to some fields in the initial page that have a button just beneath them called "Generate Assignments via Translation".  You fill out three fields:</p>
<li>About 1.5 inches up there is a field called "Save as user".  You put your user name (without master: in front of it) in that box
<li>The From box gets "homoserine kinase"
<li>The To box get "Homoserine kinase (EC"
<p>You click on the <span="code">"Generate Assignments via Translation"</span>.  This builds something called an "assignments set" under your user name. Note that no assignments have yet been made.</p>

<li>Then, you need to process the assignments set.  You do this by
going to the search form about 1.5 inches below where you were to were
it says <span="code">"Process Saved Assignment Sets"</span>.  You fill in your user name (WITH the master:) and click on <span="code">"Process Assignment Sets"</span>.</li>

<li>You will see the assignment sets that have been saved, you select one, and you "process it".  Processing an assignment set amounts to</li>

<li>checking it to make sure that you want to make those
<li>deleting the ones you don't want to make</li>
<li>making the assignments</li>
<li>deleting the assignment set</li>

<a name="edit_variants"><h2>Edit variants</h2></a>
<p>A very useful tool for managing the variants of your subsystems.</p>

<div class="code" style="text-align:center">
<A href="../set_variants.cgi">set_variants.cgi</a>

Close your subsystem before using this tool to change the variants codes.

<a name="make_trees"><h2>Make trees</h2></a>

<p>Here is how to make a tree and use it to edit annotations, as described by Ross.</p>

<li>Pick a column in one of your subsystems that contains, say, 20-50 PEGs.<br />
For myself, I am choosing TcuB: works with TcuA to oxidize tricarballylate to cis-aconitate in <a href="http://anno-3.nmpdr.org/anno/FIG/subsys.cgi?user=&ssa_name=Tricarballylate_Utilization&request=show_ssa">Tricarballylate Utilization</a>.</li>

<li>Go down to <em>For sequences in a column (i.e., role):</em> and pick the appropriate column.  Then click on <em>Align Sequences in Column</em>
<br />This may run for a while, since the program must try to construct one or mor multiple sequence alignments.</li>

<li>When it comes back, go to the very end of the subsystem stuff, and you should see one or more trees shown.  They all have numbers.  Mine is "2.1" where the "2" means "role 2" and the ".1" means the first alignment (of possibly several) constructed from the sequences in the column.</li>

<li>Now go up to  <em>Realign subgroup within a column (adding homologs):</em></li>

<li>Type in your tree number (in my case, 2.1)</li>

<li>In the box labeled <em>Include homologs that pass the following threshhold:</em> and type in "1.0e-20"  (which means look for sequences that are similar to those in the column at a cutoff of 1.0e-20)</li>

<li>Now click on <em>Realign Sequences in Column</em></li>

<li>When the page comes back, go to the bottom, select the tree you made (in my case "2.1"), and click on use_tree.</li>

<li>You are now in an environment where you can look at the phylogenetic tree, you can reroot it, or you can make assignments using it.</li>


<p>Here are some things you can do with the tree</p>

<li>If you go and change some annotations (by clicking on the leaves), you may wish to just redraw the tree with the annotations updated.  That is what Redraw tree does.</li>

<li>To reroot the tree, check a single node, and click on Reroot tree.  This will reroot the tree between the checked node and its parent.<br />This is very useful as you try to make the tree "coherent"</li>

<li>You can delete subtrees by checking their root nodes and clicking on Delete subtrees. </li>

<li>You can assign to all nodes in a subtree by checking the node, pasting in the desired assignment (at the bottom) and clicking on assign.</li>

<li>Alternatively, you can check a node (not a leaf) and a single leaf.  Then, clicking assign will assign the function from the leaf to every leaf in the subtree below the checked nonleaf.</li>

<li>You can ask that homogeneous subtrees be collapsed (this is useful as you progress in a big tree to making things consistent)</li>

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