nembase4/phylograph.shtml at master · blaxterlab/nembase4 · GitHub

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<title> www.nematodes.org - NEMBASE3 </title>
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<blockquote>
<table width=450 border=0 cellspacing=0 link="#0000FF" vlink="#0000FF">
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SimiTri</td></tr><tr><td><br>
 is a new tool currently
being developed which displays the the phylogenetic profiles for
a large number of clusters on one graphic (see examples below).
It has recently been made available to view selections of clusters
from the <a href="/nembase3/nembase.php">
annotation</a>search page.
<br><br>

How it works
For each cluster, the consensus sequence was BLASTXed against a range
of different protein databases - Archaebacteria, Drosophila, Saccharomyces
cerevisiae, C. elegans, Mus musculus, Plasmodium falciparum, Xenopus laevis,
Danio rerio, Eubacteria, Nematodes incl. C.elegans, Nematodes excl. C.elegans
and Non nematode proteins. BLAST scores in excess of 50 (our 'significance
cutoff') were extracted in addition to the highest e-value and imported
into NEMBASE.
SimiTri takes these values and uses them to draw a graphic in the
form of a three-node graph.<br><br>
To launch the
application, simply select SimiTri under the output options and select
the three databases to be used for making the comparisons. The selected
clusters will then be used to generate a graphic and a list of clusters (see
below).
<br>
<img src="/pictures/phylo.jpg">
<br>
From the above figure it can be seen that each node of the triangle represents
one set of sequences - C.elegans proteins, non-elegans nematode
proteins and non-nematode proteins. The position of a cluster
(represented as a single square coloured by the highest BLAST e-value) thus
represents its relatedness to each of the three categories (calculated
from the mean of the BLAST scores). The diagram below shows how the triangle
may be interpreted.
<br>
<img src="/pictures/venn2.jpg">
<br>
Clusters found on the three vertices indicate that they do not have
a significant blast hit against the database located on the opposite
node. Clusters which were found to be unique (no significant blast score
against the three dbs) and those which only had a significant score
for one database, are listed in a table below the graphic.<br><br>
<br>
</td></tr>
<br><br>
</table>
</blockquote>
<br><br>

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