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clean up help for abstract functional coupling

<h1>How to Read the Table Showing Abstract Coupling for a Given PEG</h1>

<p>
The table showing abstract coupling data should be thought of as a table
listing evidence that a given PEG (shown in the title of the table)
is functionally related to other PEGs.  Each line in the table corresponds
to a prediction made using some technique for generating clues.  The
meanings of the columns are as follows:

<ul>
<li> <b>coupled to</b> gives the PEG number of the "coupled to" PEG from
the same genome (e.g., if the given PEG were
fig|107806.1.peg.7, and the value in this column were 224, the "coupled to"
PEG's ID would be fig|107806.1.peg.224).
<br>
<li> <b>Score</b> is a score that should estimate the probability that the predicted coupling is real.
<br>
<li><b>Type of Coupling</b> gives the type of evidence that leads us to
generate this "clue".  The types of evidence that we currently support
are as follows:
<ul>
<br>
<li><b>IFC</b> stands for <b>indirect functional coupling</b>.
<li><b>Fusion</b>stands for a situation in which two functional domains 
sometimes occur in separate genes and sometimes in a fused form.
</ul>

<br>
<li><b>Type-specific Data</b> gives a list of 0 or more comma-separated 
data items
that depend on the specific type of coupling evidence.  The meanings of these
fields are described below.
</ul>

<h2> IFC type-specific data fields</h2>

The first two fields are PEG ids.  These two PEGs occur in another genome
(a prokaryotic genome) in which "direct functional coupling" evidence
based of preserved contiguity exists.  You can click on either link to
investigate these PEGs.  
<br>
Let us call the given PEG <b>PEG1</b>, the coupled-to PEG <b>PEG2</b>,
the first of the two directly coupled PEGS <b>PEG3</b>, and the second
of the two directly coupled PEGs <b>PEG4</b>.  Then, the indirect functional 
coupling is based on the fact that
<ul>
<li> PEG1 and PEG3 are bidirectional best hits with a similarity score
given as the third of the type-specific data items,
<br>
PEG3 and PEG4 have a co-occurence score given by the fourth type-specific 
field, and
<br>
<li> PEG2 and PEG4 are bidirectional best hits with a similarity score
given as the fifth of the type-specific data items.
</ul>

<br>
When we say that PEG3 and PEG4 have a co-occurence score of <i>n</i>,
we mean that the two PEGs occur within 5 kilobases of each other in at least
<i>n</i> genomes such that none of the collections of genomes have 
occurrences that are more than 90% identical.  That is, close strains are
not counted multiple times in arriving at this figure.

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