src/hg/makeDb/trackDb/blatFr1.html 1.8
1.8 2010/03/15 21:42:23 ann
Massive change of all instances of ($o_date/$o_db) to ($o_date). This is
because there was a recent change to hgcentral.dbDb adding much more detail to
the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by
Angie.
Index: src/hg/makeDb/trackDb/blatFr1.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/blatFr1.html,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 1000000 -r1.7 -r1.8
--- src/hg/makeDb/trackDb/blatFr1.html 10 Apr 2006 21:29:12 -0000 1.7
+++ src/hg/makeDb/trackDb/blatFr1.html 15 Mar 2010 21:42:23 -0000 1.8
@@ -1,39 +1,39 @@
<H2>Description</H2>
<P>
This track shows blat translated protein alignments of the Fugu
-($o_date/$o_db) genome assembly to the $organism genome. The
+($o_date) genome assembly to the $organism genome. The
v3.0 Fugu whole genome shotgun assembly was provided by the
<A HREF="http://www.jgi.doe.gov/index.html" TARGET=_blank>US
DOE Joint Genome Institute</A> (JGI).
</P>
<P>
The strand information (+/-) for this track is in two parts. The
first + or - indicates the orientation of the query sequence whose
translated protein produced the match. The second + or - indicates the
orientation of the matching translated genomic sequence. Because the two
orientations of a DNA sequence give different predicted protein sequences,
there are four combinations. ++ is not the same as --; nor is +- the same
as -+.</P>
<H2>Methods</H2>
<P>
The alignments were made with blat in translated protein mode requiring two
nearby 4-mer matches to trigger a detailed alignment. The $organism
genome was masked with RepeatMasker and Tandem Repeat Finder before
running blat. </P>
<H2>Credits</H2>
<P>
The
<A HREF="http://genome.jgi-psf.org/fugu6/fugu6.info.html" TARGET=_blank>
3.0 draft</A> from JGI was used in the
UCSC Fugu blat alignments. These data were provided freely by the JGI
for use in this publication only.</P>
<H2>References</H2>
<P>
Kent, W.J.
<A HREF="http://www.genome.org/cgi/content/abstract/12/4/656"
TARGET=_blank>BLAT - the BLAST-like alignment tool</A>.
<em>Genome Res.</em> <B>12</B>(4), 656-664 (2002).</P>