d7106732e0f5642c0b28736e41587a4d17a64071 luvina Mon Jun 29 11:26:13 2015 -0700 added gencode genes announcement to homepage diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 637c900..df586cf 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -24,116 +24,131 @@


	To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the genome-announce mailing list. Please see our blog for posts about Genome Browser tools, features, projects and more. + + + + 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. + + + 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). The assembly was provided by the Max-Planck Institute for Evolutionary Anthropology. There are 10,867 scaffolds with a total size of 2,869,190,071 bases. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The bonobo (panPan1) browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. - - 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. - - - Using the Data Integrator you can select up to five tracks, including custom tracks - and hub tracks, and output tab-separated text that contains all the fields from both - the first track and the overlapping items from the other track(s). If you need only - a subset of the fields from your selected tracks, the Data Integrator allows you to - choose which fields to include in the output. You can also query your current Genome - Browser position, search for positions of items such as genes, SNPs, etc. by name, - query over a set of up to 1000 positions, and even retrieve genome-wide data - (subject to data size). The Data Integrator output can be viewed in your web browser - window or downloaded to an optionally gzip-compressed file. Look for "Data Integrator" - in the Genome Browser Tools menu (top blue bar) if you'd like to try it out. - - - - For more information about the Data Integrator's capabilities and usage, see the - user's guide: - http://genome.ucsc.edu/goldenPath/help/hgIntegratorHelp.html. - As always, we welcome questions and feedback on our public mailing list: - genome@soe.ucsc.edu - - - - Thanks to Angie Hinrichs and Matthew Speir for all of their work on this feature. - - - 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. ---> 28 May 2015 - New UCSC Genes Track Released for GRCm38/mm10: We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10 mouse Genome Browser. Read more. - - - 15 May 2015 - - Work for Us! New Job Openings on the UCSC Genome Browser Project: - The UCSC Genome Browser project team is looking for two talented people to join our - engineering staff based in Santa Cruz, CA. - Read more. -

To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the genome-announce mailing list. Please see our blog for posts about Genome Browser tools, features, projects and more.

+ +

+ 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. +

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). The assembly was provided by the Max-Planck Institute for Evolutionary Anthropology. There are 10,867 scaffolds with a total size of 2,869,190,071 bases.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The bonobo (panPan1) browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

- 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. -

- -

Using the Data Integrator you can select up to five tracks, including custom tracks - and hub tracks, and output tab-separated text that contains all the fields from both - the first track and the overlapping items from the other track(s). If you need only - a subset of the fields from your selected tracks, the Data Integrator allows you to - choose which fields to include in the output. You can also query your current Genome - Browser position, search for positions of items such as genes, SNPs, etc. by name, - query over a set of up to 1000 positions, and even retrieve genome-wide data - (subject to data size). The Data Integrator output can be viewed in your web browser - window or downloaded to an optionally gzip-compressed file. Look for "Data Integrator" - in the Genome Browser Tools menu (top blue bar) if you'd like to try it out. -

- -

For more information about the Data Integrator's capabilities and usage, see the - user's guide: - http://genome.ucsc.edu/goldenPath/help/hgIntegratorHelp.html. - As always, we welcome questions and feedback on our public mailing list: - genome@soe.ucsc.edu - -

- -

Thanks to Angie Hinrichs and Matthew Speir for all of their work on this feature. -

- -

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.

--->

28 May 2015 - New UCSC Genes Track Released for GRCm38/mm10: We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10 mouse Genome Browser. Read more.

- -

- 15 May 2015 - - Work for Us! New Job Openings on the UCSC Genome Browser Project: - The UCSC Genome Browser project team is looking for two talented people to join our - engineering staff based in Santa Cruz, CA. - Read more. -