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-- 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. --

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- 1 Apr 2016 - - Going Back to Our Roots -

- For many years, the UCSC Genome Browser has provided a dynamic, cutting-edge - interface for - viewing genomic data. As time has gone by, however, it has become clear to us - that we - cannot keep this up. It is not fair to you, our users, that our interface - keeps changing, - and it has increasingly been a burden on us to keep up with emerging web - technologies. Today - that all changes, as we return you to the roots of the web: ASCII. -

- We apologize again for subjecting you to so many changes over the years, and - hope that this - new, more consistent interface will find your approval. -

- In related news, we have also revised the interface for uploading custom - tracks. Rather than - forcing you to wrestle with inconvenient file formats for your data or attempt - to set up a web server, - we now provide the option of loading your data from a deck of ISO 6586:1980 - punch cards. Simply - punch your data onto a deck and mail the deck to us. Our staff of highly - trained specialists - will take care of loading track, and will inform you by mail when the process - is complete. Please - note that our current policy of expiring unused custom tracks remains in - effect; you must visit - your track within 72 hours of the postmark date. Regrettably, decks cannot be - returned. -

- Card decks may be addressed to:
- UCSC Genome Informatics Group
- Center for Biomolecular Science & Engineering
- CBSE, 501D Engineering II Building
- University of California, Santa Cruz
- 1156 High Street
- Santa Cruz, CA 95064 -

- This new file format is also an option for data output from the UCSC Table Browser. - Simply select "mail card deck" from the "output format" menu, and then enter - your name and address on the subsequent - page. Please allow 4-6 weeks for delivery. - -

- 21 Mar 2016 - - Genome Browsers for C. elegans and Brown Kiwi Now Available -

- A Genome Browser is now available for the Caenorhabditis elegans - assembly released February 2013 by the C. elegans Sequencing Consortium - (C. elegans Sequencing Consortium version WBcel235, UCSC version ce11). - For more information and statistics about this assembly, see the NCBI assembly record - for WBcel235. - There are 7 complete chromosomes with a total size of 100,286,401 bases. -

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- Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser - FTP server or the - Downloads page. - Please observe the conditions for use when - accessing and using these data sets. The annotation tracks for this browser 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. -

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- A Genome Browser is now available for the brown kiwi (Apteryx australis) - assembly released June 2015 by the - Max-Plank Institute for Evolutionary Anthropology (MPI-EVA version AptMan0, - UCSC version aptMan1). - For more information and statistics about this assembly, see - AptMant0 in the NCBI Assembly database. There are - 24,719 scaffolds with a total size of 1,523,986,457 bases. -

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- 8 Mar 2016 - - Combine Multiple Regions of the Genome Browser into a Single Visualization! -

- Have you ever wished you could remove all of the intronic or intergenic regions from the - Genome Browser display? Have you ever dreamed of being able to visualize multiple - far-flung regions of a genome? Well, now you can with the new "multi-region" option - in the Genome Browser! -

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- The multi-region modes provide four different ways to manipulate the display. - First, we have an "exon-only" mode that allows you to - remove all of the intergenic and intronic sequences from the display, leaving you with - only the exonic regions. Next, there is the "gene-only" mode allowing you to remove only - the intergenic regions from the display, leaving the genes with exons and introns intact. - Then there is the "custom regions" mode that allows you to use a remote BED file to - specify the regions you are interested in viewing alongside each other. Lastly, for human - assemblies hg17 and newer, there is the "alternative haplotype" mode that allows you to - view a haplotype sequence inserted into its position in the reference genome. -

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- To access these exciting, new multi-region modes, first select your organism and assembly - of interest and navigate to the Genome Browser visualization. Below the tracks display, - there is a button labeled "multi-region". Clicking this button will bring up - a configuration box for the different multi-region modes. For example: -

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- From this pop-up, you will be able to switch between the different modes or exit these - multi-region modes if desired. For instance: -

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- Additionally, you can enter the "Exon-only" mode by typing the keyboard shortcut - "e" then "v". You can exit any of the multi-region modes and return to the - default Genome Browser display by typing the keyboard shortcut "d" then "v". -

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- For more information about each individual multi-region mode, please see the - User Guide. -

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- Thank you to Galt Barber, Matthew Speir, and the entire UCSC Genome Browser quality assurance team for - all of their efforts in creating these exciting new display modes. -

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- 10 February 2016 - - Two New Assemblies Now Available in the Genome Browser: - Genome Browsers are now available for the mouse lemur - (Microcebus murinus) - and platypus (Ornithorhynchus anatinus) assemblies. - Read more. -

- - 20 Jan 2016 — - dbSNP 142 Available for mm10 - Read more. -

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- 4 Apr 2016 - - New video shows how to obtain sequence or coordinates for exons. -

- We have released a new video to our YouTube channel. This newest installment in our effort - to share the capabilities of the Genome Browser shows how to - use the Table Browser to obtain either the sequences or the coordinates for - exons in the genes from a chosen region of the genome. -

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- We also want to take this opportuinty to remind you that we offer - on-site workshops to help you and your colleagues make the most out - of the Genome Browser. -

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