UCSC Genome Bioinformatics
Genome Browser
Blat
Table Browser
Gene Sorter
In Silico PCR
Genome Graphs
Galaxy
VisiGene
Utilities
Downloads
Release Log
Custom Tracks
Cancer Browser
Microbial Genomes
ENCODE
Neandertal
Mirrors
Training
Blog
Credits
Publications
Cite Us
Licenses
Jobs
Staff
Contact Us

  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.

Give to the UCSC Genome Browser

  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.


08 April 2015 - bigGenePred Format Now Supported in the Genome Browser

We are pleased to announce that the UCSC Genome Browser now supports data in bigGenePred format. bigGenePred format stores annotation items that are a linked collection of exons, much as BED files do, but bigGenePred has additional information about the coding frames and other gene specific information. bigGenePred files are created initially from BED-type files with some extra fields, using the program bedToBigBed with a special AutoSQL file that defines the fields of the bigGenePred. The resulting bigBed files are in an indexed binary format. The advantage of these bigBed files is that only portions of the files needed to display a particular region are transferred to UCSC. So for large data sets, bigBed is considerably faster than regular BED files.

This new format is available for use in custom tracks and data hubs. For more information about bigGenePred, please see our bigGenePred Track Format help page.


02 April 2015 - New Tarsier (tarSyr2) Assembly Now Available in the Genome Browser

We are pleased to announce the release of a Genome Browser for the September 2013 assembly of tarsier, Tarsius syrichta (WashU Tarsius_syrichta-2.0.1, UCSC version tarSyr2). The whole genome shotgun assembly was provided by Washington University. There are 337,189 scaffolds with a total size of 3,453,864,774 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 tarsier (tarSyr2) 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.


02 April 2015 - New Training Video!

Going crazy counting amino acids? Learn an easier way to find the codon number in our new training video. See our training page, and our YouTube channel for details.


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.


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. Read more.

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. 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.