6a89c12dbd7cc73c93e8be489d4e7fedf8b06670 jnavarr5 Mon Aug 3 16:25:26 2026 -0700 Fixing dead and unstable publisher links, refs #37986 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index c717f432ddb..d420173c47f 100644 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -19414,31 +19414,31 @@ <p> The goal of the Lowe Lab is to make the Archaeal Genome Browser Database a forum for ongoing community-based genome annotation, and they welcome new experimental and bioinformatic analyses. If you would like to contribute data, or have questions or feedback about the database, contact <a href="mailto:lowe@soe.ucsc.edu">Todd Lowe</a>.</p> <a name="040808"></a> <h2>Apr. 8, 2008 Updated Cow Genome Browser now available</h2> <p> The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Oct. 2007 draft assembly of the Cow genome <em>Bos taurus</em>. This assembly (UCSC version bosTau4) was produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC) as Baylor release Btau_4.0.</p> <p> The Btau_4.0 release was produced using the -<a href="http://www.genome.org/cgi/content/abstract/14/4/721">Atlas</a> genome assembly system at +<a href="https://genome.cshlp.org/content/14/4/721">Atlas</a> genome assembly system at BCM HGSC. The sequencing strategy combined BAC shotgun reads with whole genome shotgun reads from small insert libraries as well as BAC end sequences. The assembly contains chromosomes 1-29 and X as well as 11869 scaffolds (named chrUn.004.*). The mitochondrial sequence (available in the browser as "chrM") was obtained from GenBank accession GI:60101824.</p> <p> The Btau_4.0 assembly was tested against available bovine sequence data sets (EST sequences and finished BAC sequences) for extent of coverage (completeness). When assembled contigs were tested, over 95% of the sequences in these data sets were found to be represented, indicating that the shotgun libraries used to sequence the genome were comprehensive. Of the 1.04 million EST sequences 95.0% were contained in the assembled contigs. Assuming the ESTs are uniformly distributed throughout the genome, the estimated genome size is 2.73Gb/95% = 2.87Gb. For detailed information on the sequencing and assembly techniques, see the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/bovine/" target="_blank">Bovine Genome Project</a> web page.</p> <p> @@ -19491,31 +19491,31 @@ bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs. The company has its headquarters in Seattle, with offices in San Francisco and Boston. Further information can be found at www.openhelix.com or by calling 1-888-861-5051.</p> <a name="031008"></a> <h2>Mar. 10, 2008 Orangutan Genome Browser now available</h2> <p> The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Jul. 2007 draft assembly of the Sumatran orangutan genome, <em>Pongo pygmaeus abelii</em>. This assembly (UCSC version ponAbe2, WUSTL version Pongo_albelii-2.0.2) was provided by the Genome Sequencing Center at Washington University School of Medicine in St. Louis (WUSTL), MO, USA.</p> <p> The orangutan genome was sequenced to 6X coverage using a female orangutan known as "Susie" from the Gladys Park Zoo (Brownsville, TX, USA). The combined sequence reads were -assembled using <a href="http://www.genome.org/cgi/content/abstract/13/9/2164" +assembled using <a href="https://genome.cshlp.org/content/13/9/2164" target="_blank">PCAP</a> and filtered for all known non-orangutan sequence contaminants. For more details about the assembly, see the orangutan browser <a href="../cgi-bin/hgGateway?db=ponAbe2">gateway</a> page and the WUSTL <a href="http://genome.wustl.edu/genome.cgi?GENOME=Pongo%20abelii" target="_blank"><em>Pongo abelii</em></a> web page.</p> <p> Of the 3.09 Gb of total sequence, 3.08 Gb are ordered and oriented along the chromosomes. Gap sizes between supercontigs were estimated based on their size in human, with a maximum gap size of 30 kb allowed. For a list of the chromosomes in this assembly, click the "Sequences" link on the orangutan browser <a href="../cgi-bin/hgGateway?db=ponAbe2">gateway</a> page. The mitochondrial sequence is also available as the virtual chromosome "chrM".</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ponAbe2">FTP server</a> or <a href="http://hgdownload.gi.ucsc.edu/downloads.html#orangutan">Downloads</a> page. These data @@ -19829,31 +19829,31 @@ <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/phastCons28way">conservation</a>) or from the <a href="http://hgdownload.gi.ucsc.edu/downloads.html#human">Downloads page</a>.</p> <p> The previous 17-vertebrate versions of the Conservation and Most Conserved tracks remain available on the hg18 Genome Browser as the "17-Way Cons" and "17-Way Most Cons" tracks.</p> <a name="061307"></a> <h2>Jun. 13, 2007 ENCODE findings released to public</h2> <p> The findings of the ENCODE project have been released to the public today, the culmination of a four-year effort to catalog the biologically functional elements in 1 percent of the human genome. The publications, which include a group paper in the 14 June 2007 issue of <a href="http://www.nature.com/nature/journal/v447/n7146/full/nature05874.html" target="_blank"><em>Nature</em></a> and 28 companion papers in the June 2007 issue of -<a href="http://www.genome.org/content/vol17/issue6/" target="_blank"><em>Genome Research</em></a>, +<a href="https://genome.cshlp.org/content/17/6" target="_blank"><em>Genome Research</em></a>, were authored by researchers from academic, governmental, and industry organizations located in 11 countries. The <em>Nature</em> issue includes a pull-out poster featuring a screenshot of the UCSC Genome Browser displaying a broad range of the ENCODE data.</p> <p> In the <a href="http://genome.gov/25521554" target="_blank">press release</a> accompanying the publication rollout, NHGRI Director Francis S. Collins is quoted as saying "This impressive effort has uncovered many exciting surprises and blazed the way for future efforts to explore the functional landscape of the entire human genome. Because of the hard work and keen insights of the ENCODE consortium, the scientific community will need to rethink some long-held views about what genes are and what they do, as well as how the genome's functional elements have evolved. This could have significant implications for efforts to identify the DNA sequences involved in many human diseases."</p> <p> The main portal for the ENCODE data is the UCSC ENCODE Genome Browser. The analysis effort has been coordinated by <a href="http://wwww.ensembl.org/" target="_blank">Ensembl</a>. Much of the primary