src/hg/makeDb/trackDb/parsPValues.html 1.2

Index: src/hg/makeDb/trackDb/parsPValues.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/parsPValues.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/makeDb/trackDb/parsPValues.html	22 Dec 2002 09:31:02 -0000	1.1
+++ src/hg/makeDb/trackDb/parsPValues.html	21 May 2010 18:52:21 -0000	1.2
@@ -1,24 +1,24 @@
 <H2>Description</H2>
 <P>This track displays the level conservation of the Zoo sequences at any given position. More precisely, it computes the p-value of observing a certain parsimony score for a given column of the multiple alignment, under the null model of neutral evolution.</P>
 <H2>Methods</H2>
 <P>
 1) Adam Siepel has inferrred the phylogenetic tree relating the Zoo
 species, as well as the length of each branches of the tree. I use this
 tree to measure the surprise of the conservation observed.
 </P>
 <P>
 2) For each column of the multiple alignment produced by Webb Miller, we
 compute the parsimony score for the columm, using Adam's phylogenetic
 tree. We then compute a p-value for that parsimony score, under a null
 model of neutral evolution (see below for a description of this null
 model). Species with gaps in the column are ignored. A column will get a
 low p-value if the parsimony score for the set of non-gap species is
 surprisingly low, given the divergence of these species. For column i, let
 Xi be the negative log of the p-value for that column.
 </P>
 <p>
 3) For position i of the alignment, the score plotted on the track is the
-average of the Xj's in a window of 10bp around position i.
+average of the Xj's in a window of 10 bp around position i.
 </P>
 <H2>Credits</H2>
 <P>Many thanks to Adam Siepel for the phylogenetic inferrences and to Webb Miller for providing the multiple alignment of the Zoo sequences.</P>