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  About the UCSC Genome Bioinformatics Site

Welcome to the UCSC Genome Browser website. This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to ENCODE data at UCSC (2003 to 2012) and to the Neandertal project. Download or purchase the Genome Browser source code, or the Genome Browser in a Box (GBiB) at our online store.

We encourage you to explore these sequences with our tools. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways. Blat quickly maps your sequence to the genome. The Table Browser provides convenient access to the underlying database. VisiGene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns. Genome Graphs allows you to upload and display genome-wide data sets.

The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the UC Santa Cruz Genomics Institute at the University of California Santa Cruz (UCSC). If you have feedback or questions concerning the tools or data on this website, feel free to contact us on our public mailing list.

The Genome Browser project team relies on public funding to support our work. Donations are welcome -- we have many more ideas than our funding supports! If you have ideas, drop a comment in our suggestion box.

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  NewsFollow @GenomeBrowser on Twitter Genome Browser Facebook page

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.

01 April 2015 - New GRCz10 Zebrafish Assembly Now Available

The most recent zebrafish assembly -- GRCz10 (UCSC version danRer10, Sep. 2014) -- is now available in the UCSC Genome Browser. This is the first zebrafish release by the Genome Reference Consortium, who took over the improvement and maintenance of the zebrafish genome assembly.

The GRCz10 assembly improves upon Zv9 by utilizing optical mapping and additional meiotic mapping to fill gaps with new clone sequence and improve the positioning of assembly components. This has also been supplemented with a new whole genome shotgun assembly WGS31. The result is an assembly with a sequence length of 1.3 Gb in 26 chromosomes and 1,035 scaffolds. For more details about the GRCz10 assembly, see the GRCz10 assembly page or the official GRCz10 announcement.

The danRer10 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page.

We'd like to thank the Genome Reference Consortium for providing this assembly. The UCSC zebrafish Genome Browser was produced by Hiram Clawson, Brian Raney and Steve Heitner. See the credits page for a detailed list of the organizations and individuals who contributed to this release.

20 March 2015 - New Visualization Option for RepeatMasker

We are excited to announce the release of the new RepeatMasker Visualization track for the hg38 and mm10 assemblies. This new RepeatMasker track displays detailed information that includes the amount of unaligned repeat sequence and lines joining repeat fragments. Additionally, repeats are now colored based on their repeat class. This new RepeatMasker track incorporates a new details page that includes the detailed RepeatMasker output and the raw alignment used to generate the final repeat annotation. You can read more about this track on the description page for either hg38 or mm10.

This track is the result of a collaboration between the Institute for Systems Biology and the UCSC Genome Browser. We would like to thank Robert Hubley, Arian Smit, Hiram Clawson, and Matthew Speir for their efforts in creating this track.

03 March 2015 - Use UDR for Quick Sizable Downloads: The UCSC Genome Browser is pleased to share a download protocol to use when downloading large sets of files from our download servers: UDR (UDT Enabled Rsync). UDR utilizes rsync as the transport mechanism, but sends the data over the UDT protocol, which enables huge amounts of data to be downloaded efficiently over long distances. Read more.

26 February 2015 - New Training Video! View it now on our YouTube channel. Read more.

  Conditions of Use

The Genome Browser software, sequence and annotation data are freely available for use with these conditions. A license is required for commercial use of the software. For assistance with questions or problems regarding the UCSC Genome Browser software, database, genome assemblies, or release cycles, click here.

Program-driven use of this software is limited to a maximum of one hit every 15 seconds and no more than 5,000 hits per day.

The UCSC Genome Browser was created by the Genome Bioinformatics Group of UC Santa Cruz. Software Copyright (c) The Regents of the University of California. All rights reserved.