src/hg/makeDb/trackDb/xenoBestMrna.html 1.12
1.12 2010/01/23 00:53:45 ann
Finally decided to take the plunge and edit the citations for the genbank
references.
Index: src/hg/makeDb/trackDb/xenoBestMrna.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/xenoBestMrna.html,v
retrieving revision 1.11
retrieving revision 1.12
diff -b -B -U 1000000 -r1.11 -r1.12
--- src/hg/makeDb/trackDb/xenoBestMrna.html 20 Sep 2007 02:24:07 -0000 1.11
+++ src/hg/makeDb/trackDb/xenoBestMrna.html 23 Jan 2010 00:53:45 -0000 1.12
@@ -1,68 +1,68 @@
<H2> Description</H2>
<P>
This track displays translated blat alignments of vertebrate and
invertebrate mRNA in
<A HREF="http://www.ncbi.nlm.nih.gov/Genbank/index.html"
TARGET=_blank>GenBank</A> from organisms other than $organism.
Better alignments are indicated by darker coloration in the display.</P>
<H2>Methods</H2>
<P>
The mRNAs were aligned against the $organism genome using translated blat.
When a single mRNA aligned in multiple places, the alignment having the
highest base identity was found. Only those alignments having a base
identity level within 1% of the best and at least 25% base identity with the
genomic sequence were kept.</P>
<H2>Using the Filter</H2>
<P>
This track has a filter that can be used to change the display mode,
change the color, and include/exclude a subset of items within the track.
This may be helpful when many items are shown in the track display,
especially when only some are relevant to the current task.
The filter is located at the top of the track description page, which is
accessed via the small button to the left of the track's graphical
display or through the link on the track's control menu.
To use the filter:
<OL>
<LI>Type a term in one or more of the text boxes to filter the mRNA
display. For example, to apply the filter to all mRNAs expressed in the
liver, type "liver" in the tissue box. To view the list of
valid terms for each text box, consult the table in the Table Browser that
corresponds to the factor on which you wish to filter. For example, the
"tissue" table contains all the types of tissues that can be
entered into the tissue text box. Multiple terms may be entered at once,
separated by a space. Wildcards may also be used in the
filter.
<LI>If filtering on more than one value, choose the desired combination
logic. If "and" is selected, only mRNAs that match all filter
criteria will be highlighted. If "or" is selected, mRNAs that
match any one of the filter criteria will be highlighted.
<LI>Choose the color or display characteristic that should be used to
highlight or include/exclude the filtered items. If "exclude" is
chosen, the browser will not display mRNAs that match the filter criteria.
If "include" is selected, the browser will display only those
mRNAs that match the filter criteria.
</OL></P>
<P>
When you have finished configuring the filter, click the <em>Submit</em>
button.</P>
<H2>Credits</H2>
<P>
The mRNA track was produced at UCSC from mRNA sequence data
submitted to the international public sequence databases by
scientists worldwide.</P>
<H2>References</H2>
<P>
-Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and
-Wheeler, D.L.
-<A HREF="http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D23"
-TARGET=_blank>GenBank: update</A>. <em>Nucleic Acids Res.</em> <B>32</B>,
-D23-6 (2004).</P>
+Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J,
+Wheeler DL.
+<A HREF="http://nar.oupjournals.org/cgi/content/abstract/32/suppl_1/D23"
+TARGET=_blank>GenBank: update</A>. <em>Nucleic Acids Res.</em>
+2004 Jan 1;32(Database issue):D23-6.</P>
<P>
-Kent, W.J.
+Kent WJ.
<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>
+<em>Genome Res.</em> 2002 Apr;12(4):656-64.</P>