3d46fcbd6ff3db6ac5daeef908677c774757ec9a
cath
Tue Feb 9 16:30:07 2016 -0800
Editing static pages to include micMur2 & ornAna2 refs #15098
diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html
index 61e4178..ecc78ea 100755
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@@ -1,142 +1,154 @@
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<font size="4"><a name="TOC"></a><b> News</b></font><a href="http://www.twitter.com/GenomeBrowser" target="_blank"><img src="http://twitter-badges.s3.amazonaws.com/t_small-a.png" title="Follow @GenomeBrowser on Twitter" alt="Follow @GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a>
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target="_blank"><img
src="/images/FB-f-Logo__blue_22.jpg"
style="vertical-align:text-bottom; margin-left: 15px;"
alt="Genome Browser Facebook page"></a>
<a href="https://plus.google.com/107643636314131661344" rel="publisher"></a>
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SRC="images/news.jpg" ALT="" ALIGN="right" BORDER=0></A>
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<P>
To receive announcements of new genome
assembly releases, new software features, updates and
training seminars by email, subscribe to the
<A HREF="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en"
TARGET=_blank>genome-announce</A> mailing list. Please see our
<a href="http://genome.ucsc.edu/blog"
target=_blank>blog</a> for posts about Genome Browser tools, features, projects and more.
</p>
<!-- start news -->
+<p>
+ <font color="#006666" size="4"><b> 9 February 2016 -
+ Two New Assemblies Now Available in the Genome Browser</b></font>
+ <p>
+ A Genome Browser is now available for the mouse lemur (<em>Microcebus murinus</em>)
+ assembly released May 2015 by the
+<A HREF="http://www.broadinstitute.org/scientific-community/science/projects/mammals-models/29-mammals-project"
+TARGET="_blank">The Broad Institute</A> and the
+<A HREF="https://www.hgsc.bcm.edu/non-human-primates/mouse-lemur-genome-project"
+TARGET="_blank">Baylor College of Medicine Human Genome Sequencing Center</A>
+ For more information and statistics about this assembly, see the NCBI assembly record
+ for <a href="http://www.ncbi.nlm.nih.gov/assembly/329621" target="_blank"> Mmur_2.0</a>.
+There are 10,311 scaffolds with a total size of 2,438,804,424 bases.
+ </p>
+
+ <p>
+ Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
+ <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/micMur2/">FTP server</a> or the
+ <a href="http://hgdownload.soe.ucsc.edu/downloads.html#mouse_lemur">Downloads</a> page.
+ Please observe the <a href="credits.html#mouse_lemur_use">conditions for use</a> when
+ accessing and using these data sets. The annotation tracks for this browser were
+ generated by UCSC and collaborators woldwide. See the <a
+ href="credits.html#mouse_lemur_credits">Credits</a> page for a detailed list of the
+ organizations and individuals who contributed to this release.
+ </p>
+ ---
+ <p>
+ A Genome Browser is now available for the platypus (<em>Ornithorhynchus anatinus</em>)
+ assembly released February 2007 by the
+<A HREF="http://genome.wustl.edu/genomes/detail/ornithorhynchus-anatinus/"
+TARGET=_blank>Genome Sequencing Center at Washington University, St. Louis</A>.
+For more information about this assembly, see
+<A HREF="http://www.ncbi.nlm.nih.gov/assembly/237598/" TARGET="_blank">
+Ornithorhynchus_anatinus-5.0.1</A> in the NCBI Assembly database. There are
+201,525 scaffolds with a total size of 1,996,826,513 bases.
+ </p>
+
+ <p>
+ Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
+ <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ornAna2/">FTP server</a> or the
+ <a href="http://hgdownload.soe.ucsc.edu/downloads.html#platypus">Downloads</a> page.
+ Please observe the <a href="credits.html#platypus_use">conditions for use</a> when
+ accessing and using these data sets. The annotation tracks for this browser were
+ generated by UCSC and collaborators woldwide. See the <a
+ href="credits.html#platypus_credits">Credits</a> page for a detailed list of the
+ organizations and individuals who contributed to this release.
+ </p>
+
<hr>
<font color="#006666" size="4"><b>20 Jan 2016
- dbSNP 142 Available for mm10</b></font>
<p>
Data from dbSNP build 142 is now available for the most recent mouse
assembly (mm10/GRCm38). As was the case for previous annotations
based on dbSNP data, there are three tracks in this release.
One is a track containing all mappings of reference SNPs to the
mouse assembly, labeled "All SNPs (142)". The other two tracks
are subsets of this track and show different interesting and
easily defined subsets of dbSNP:
</p>
<ul>
<li>Common SNPs (142): uniquely mapped variants that appear in
at least 1% of the population
<li>Mult. SNPs (142): variants that have been mapped to more
than one genomic location
</ul>
<p>
By default, only the Common SNPs (142) are visible. The other
tracks can be made visible using the track controls.
These three SNPs (142) tracks can be found on the Mouse Dec.
2011 (mm10/GRCm38) browser in the "Variation and Repeats" group.
</p>
Thank you to the <a href="http://www.ncbi.nlm.nih.gov/SNP/">
dbSNP</a> group at NCBI for making these data publicly available.
The tracks were produced at UCSC by Brian Raney, Angie Hinrichs
and Matthew Speir.
</p>
<hr>
- <p>
- <font color="#006666" size="4"><b> 08 January 2016 -
- dbSNP 144 Available for hg19 and hg38</b></font>
- <p>
- We are pleased to announce the release of four tracks derived
- from NCBI <a href="http://www.ncbi.nlm.nih.gov/SNP/">
- dbSNP</a> Build 144 data, available on the two most
- recent human assemblies GRCh37/hg19 and GRCh38/hg38.
- </p>
- <p>
- There are four SNP tracks available as part of this release.
- One is a track containing all mappings of reference SNPs
- to the human assembly, labeled "All SNPs (144)".
- The other three tracks are subsets of this track
- and show interesting and easily defined subsets of dbSNP:
- </p>
+<!-- start archives -->
+<!--staged for future release
- <ul>
- <li>Common SNPs (144): uniquely mapped variants that appear
- in at least 1% of the population or are 100% non-reference</li>
- <li>Flagged SNPs (144): uniquely mapped variants, excluding
- Common SNPs, that have been flagged by dbSNP as
- "clinically associated"</li>
- <li>Mult. SNPs (144): variants that have been mapped to more
- than one genomic location</li>
- </ul>
<p>
- By default, only the Common SNPs (144) are visible;
- other tracks must be made visible using the track controls.
- You will find the other SNPs (144) tracks on both
- of GRCh37/hg19 and GRCh38/hg38 browsers in the "Variation" group.
- </p>
+ <font color="#006666" size="4"><b> 21 December 2015 -
+ Two New Assemblies Now Available in the Genome Browser</b></font>
<p>
- The tracks were produced at UCSC by Angie Hinrichs and
- Luvina Guruvadoo. We'd like to thank the dbSNP group at
- NCBI for providing access to these data.
+ Genome Browsers are now available for the mouse lemur
+ (<em>Microcebus murinus</em>)
+ and platypus (<i>Ornithorhynchus anatinus</i>) assemblies.
+ <a href="goldenPath/newsarch.html#021016">Read more</a>.
</p>
- <hr>
-<!-- start archives -->
-<!--staged for future release
+
<font color="#006666" size="4"><b>20 Jan 2016 —
dbSNP 142 Available for mm10</b></font>
<a href="goldenPath/newsarch.html#012016">Read more</a>.
</p>
-
+-->
<p>
<font color="#006666" size="4"><b>08 January 2016 —
- dbSNP 144 Available for hg19 and hg38
+ dbSNP 144 Available for hg19 and hg38 </font></b>
<a href="goldenPath/newsarch.html#010816">Read more</a>.
</p>
--->
<p>
<font color="#006666" size="4"><b> 21 December 2015 -
Two New Assemblies Now Available in the Genome Browser</b></font>
<p>
Genome Browsers are now available for the frog (<em>Xenopus tropicalis</em>)
and cat (<i>Felis catus</i>) assemblies.
<a href="goldenPath/newsarch.html#122115">Read more</a>.
</p>
- <p>
- <font color="#006666" size="4"><b>16 December 2015 —
- Output from Related Tables Now Available in the Data Integrator</b>: </font>
- You can now obtain data from these related tables in your output from the
- <a href="cgi-bin/hgIntegaror">Data Integrator</a>.
- <a href="goldenPath/newsarch.html#121615">Read more</a>.
- </p>
-
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