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  About the PSU Genome Bioinformatics Site

This is a version of the UCSC Genome Browser that is customized and maintained by the Penn State University Center for Comparative Genomics and Bioinformatics (PSU CCGB). It contains many tracks from the UCSC Genome Browser, and others are tracks produced and/or compiled here at PSU.


  News

27 June 2011 - Tasmanian Devil browser released

The Tasmanian Devil has been added to the browser. It contains the reads for Cedric, Spirit, and Spirit's tumor. Also a mirror of the opossum browser has been added, and includes 2 tracks from the Tasmanian Devil data, one for SNPs and another for SAPs to be viewed along with the opossum annotations. This is published in:

  • Miller, W. et al. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proceedings of the National Academy of Sciences. (27 June 2011).


12 August 2010 - bedDetail track type expanded

The bedDetail format is now available for both custom and resident tracks and allows the bed portion of the table to contain anywhere from 4 to 12 fields. bedDetail format.


2 August 2010 - Added new custom track type

A new type of custom track has been added. The personal genome SNPs (pgSnp) format is now available for custom tracks. This will do the coloring by frequency/read count and the changing of alleles to match the views just as the Genome Variants track does. It also computes amino acid changes for coding SNPs and displays them on the details page along with the amino acid properties. For more information see the personal genome SNPs format.


22 July 2010 - Added new custom track type

A new type of custom track has been added. It extends the bed format adding an ID and description to be used on the detail page displays. This format is used by HbVar query results when displayed in this browser. For more information see the bedDetail format.


19 May 2010 - Presentation at Human Variome Meeting

SNP Data Integration Using Genome Browsers


18 Feb. 2010 - New personal genomes released

Two complete genomes and three exomes of southern African men have been sequenced. Differences in these genomes from the human reference sequence are now available in the Genome Variants track. Mapped sequence reads can be viewed. Additional variation data include genotype results (1M SNP Illumina arrays) and phenotype information from PhenCode and SNPedia. The SNPs are available on both the Mar. 2006 and Feb. 2009 assemblies of the human genome, but supporting tracks are only included for the Mar. 2006 assembly. These results are published in:

  • Schuster S.C., et al. Complete Khoisan and Bantu genomes from southern Africa. Nature 463, 841-990 (18 February 2010). PMID 20164927

For downloading large sets of data please use the Galaxy library or the FTP site for aligned reads.


December, 2009

New information from Penn State labs includes the ChIP-chip and ChIP-seq data on GATA1 and TAL1 occupancy and histone modifications in a mouse erythroid cell line (without and with the critical transcription factor GATA1). These results are published in:


  Conditions of Use

The sequence and annotation data displayed in the Genome Browser are freely available for any use with the following conditions:

  • Genome sequence data use restrictions are noted within the species sections on the Credits page.
  • Some annotation tracks contributed by external collaborators contain proprietary data that have specific use restrictions. To check for restrictions associated with a particular genome assembly, review the database/README.txt file in the assembly's downloads directory.

The Genome Browser and Blat software are free for academic, nonprofit, and personal use. A license is required for commercial use. See the Licenses page for more information.

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.

For assistance with questions or problems regarding the UCSC Genome Browser software, database, genome assemblies, or release cycles, see the FAQ.



  Technical Information About the Assembled Sequence