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<h1>Comparing Regions Between Genomes</h1>

The <b>Compare Region tool</b> displays the corresponding regions in closely related genomes.

When you click on the <b>To Compare Region</b> link, close homologs of the query
gene (the gene you are positioned on) in other genomes are identified and
displayed with the corresponding 16-kb chromosomal regions aligned
around them.  If the system cannot locate at least one other genome to
present, you will see a short message indicating that fact.  If it can
find one or more such genomes, you will be shown a graphical
representation of the corresponding regions, where homologous genes
are shown by arrows with matching colors and numbers.  The query gene
is colored red, genes not conserved within the region are grey.
Although this display is very similar to the output of the Functional
Coupling, please keep in mind that the two tools are conceptually very
different.  While Compare Region simply shows immediate neighborhoods
of the closest homologs of the query gene in other genomes, regardless
of the presence/absence of any other genes in their vicinity; the FC
display includes only those genomes in which conserved gene
arrangement around the query gene is preserved.

<p>
There are two parameters worth discussing:
<ol>
<li>The size of the regions displayed defaults to 16,000 bp (8,000 bp
either side of the given gene).  You can alter this to get larger or
smaller regions.
<li>The maximum number of displayed genomes defaults to 5.  If you
wish to look at more, bump this up and a click on the <b>Resubmit</b>
button.
</ol>


<p>
If you click on any of the genes in the displayed graphic, you will shift focus to 
that gene (i.e., you will move to a protein page centered on that gene).
If you continually move to the right in the same genome, this amounts to
"walking the chromosome".  There is one important thing to note, however: if
you click on a gene from the reverse strand, it will re-orient the display
(flipping the direction).  You should either always click on genes
on the forward strand, or very carefully remember which direction you are
walking.
<p>
By clicking on the <b>Commentary</b> button, you will get a summary of the
annotations for each color group (set of similar genes).  Scrolling to
the bottom of the Commentary page will bring up the legend, which 
<ul>
<li>
explains genome abbreviations, 
<li> lists all homologous proteins groups present in each genome, and 
<li> allows selection of specific
genomes for a modified display.  
</ul>

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