21635cdb9d8d23fe98692522adf6916dfcb2c364 jcasper Thu Sep 10 16:44:05 2015 -0700 Removing release tags related to 100-way and pushing announcement, refs #14560 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 6479d23..7cbee33 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,146 +1,121 @@

News

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+ 10 September 2015 — + 100 Species Conservation Track now available on GRCh38/hg38 +

+ We are pleased to announce the release of a new Conservation track based on the human + (GRCh38/hg38) assembly. This track shows multiple alignments of 100 vertebrate species and + measurements of evolutionary conservation using two methods (phastCons and phyloP) from the + PHAST package for all species. The multiple alignments were generated using multiz and other + tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. + Conserved elements identified by phastCons are also displayed in this track. For more + details, visit the + track description page. +

+ We would like to thank Hiram Clawson and Jonathan Casper for their efforts in creating this track. +

+ +

12 August 2015 — New blog post: How to share your UCSC screenthoughts

Do you want to save your UCSC Browser screenthoughts, or share them with a colleague, or make a slide for a talk, or publish them in a paper? Saving the state of your screen can take two forms: static or dynamic. You can snap and save a picture of the screen, or you can share a link to an active Genome Browser. We talk about both approaches here and discuss some of the advantages and pitfalls of each.

- 29 June 2015 — - GENCODE Genes Now the Default Gene Set on the Human (GRCh38/hg38) Assembly -

- In a move towards standardizing on a common gene set within the bioinformatics - community, UCSC has made the decision to adopt the GENCODE set of gene models - as our default gene set on the human genome assembly. Today we have released - the GENCODE v22 comprehensive gene set as our default gene set on human - genome assembly GRCh38 (hg38), replacing the previous default UCSC Genes set - generated by UCSC. To facilitate this transition, the new gene set employs - the same familiar UCSC Genes schema, using nearly all the same table names - and fields that have appeared in earlier versions of the UCSC set. -

- By default, the browser displays only the transcripts tagged as "basic" by the - GENCODE Consortium. These may be found in the track labeled "GENCODE Basic" in - the Genes and Gene Predictions track group. However, all the transcripts in the - GENCODE comprehensive set are present in the tables, and may be viewed by - adjusting the track configuration settings for the All GENCODE super-track. - The most recent version of the UCSC-generated genes can still be accessed in - the track "Old UCSC Genes". -

- The new release has 195,178 total transcripts, compared with 104,178 in the - previous version. The total number of canonical genes has increased from - 48,424 to 49,534. Comparing the new gene set with the previous version: -

9,459 transcripts did not change.
22,088 transcripts were not carried forward to the new version.
43,681 transcripts are "compatible" with those in the previous set, - meaning that the two transcripts show consistent splicing. In most cases, - the old and new transcripts differ in the lengths of their UTRs.
28,950 transcripts overlap with those in the previous set, but do not - show consistent splicing (i.e., they contain overlapping introns with - differing splice sites)

- More details about the new GENCODE Basic track can be found on the - - GENCODE Basic track description page. -

- -

29 June 2015 — GENCODE Genes Now Default Gene Set on the Human (GRCh38/hg38) Assembly: In a move towards standardizing on a common gene set within the bioinformatics community, UCSC has made the decision to adopt the GENCODE set of gene models as our default gene set on the human genome assembly. Read more.

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26 June 2015 — New Bonobo (panPan1) Assembly Now Available in the Genome Browser: We are pleased to announce the release of a Genome Browser for the May 2012 assembly of bonobo, Pan paniscus (Max-Planck Institute panpan1, UCSC version panPan1). Read more.

- 12 June 2015 — - Data Integrator: - Have you ever wished that the Table Browser could associate your custom track items - with some other track, while retaining the item names from both? We have released a - new tool that can do just that, and more: the Data Integrator. - Read more. -