The genome has been sequenced using 454 FLX sequencing to 3X coverage (DNA derived from six female sheep each sequenced with 0.5X coverage). Contigs were assembled based on alignment to the bovine genome and ordered into ovine chromosomes using BAC-end sequences and the virtual sheep genome.
We'd like to thank the International Sheep Genomics Consortium (ISGC) sequencing center and Justus-Liebig-University for providing this assembly. We'd also like to acknowledge the UCSC team who worked on this release: Chin Li, Greg Roe, and Luvina Guruvadoo. The sheep browser annotation tracks were generated by UCSC and collaborators worldwide.
- 04 March 2011 - The Meaning of Red: Consensus on color scheme for CNVs -
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04 March 2011 - The Meaning of Red: Consensus on color scheme for CNVs: Consensus was reached on color standards to represent CNV loss (red) and gain (blue) in genomics databases by DGV, NCBI, DECIPHER, UCSC and ISCA during the 1st annual ISCA Scientific Conference. -
-- At the recent ISCA Scientific Conference in Atlanta, GA, Nigel Carter, - representing DECIPHER, made a plea for a standardized color scheme for - representation of CNV loss (deletion) or gain (duplication). Discussions - in person and by email with leaders of major CNV/genomic databases (including - DGV, dbVar, ISCA, and the UCSC Genome Browser) resulted in the recommendation - to utilize red to represent loss/deletion (consistent with the original - convention for CGH on metaphase chromosomes) and blue to represent - gain/duplication (avoiding green which is difficult for color-blind - individuals to discriminate from red). -
-- Announcement reprinted from the website for the International Standards for - Cytogenomic Arrays (ISCA) - Consortium. The UCSC Genome Browser is now conforming to this standard for the - DECIPHER track and the DGV track on human assemblies (which was released today) and - on any future tracks derived from dbVar. -
-- Thanks to Nigel Carter, Steve Scherer, Deanna Church, Angie Hinrichs, Fan Hsu, - Pauline Fujita and Robert Kuhn. -
+ Read more + -- 01 March 2011 - Updated Chimpanzee Browser Released
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01 March 2011 - Updated Chimpanzee Browser Released: We are happy to announce the release of a Genome Browser for the latest release of the chimpanzee (Pan - troglodytes) genome. The Oct. 2010 assembly -- CGSC - v2.1.3, UCSC version panTro3 -- was produced by the - Chimpanzee Sequencing and Analysis - Consortium.
-- This assembly covers about 97 percent of the genome and is - based on 6X sequence coverage. It comprises 192,898 contigs - with an N50 length of 44 kb and 33,990 supercontigs with an - N50 length of 8.4 Mb. - Improvements introduced with the 2.1.3 assembly include the - addition of over 300,000 finishing reads and the merging in - of 640 finished BACS. Approximately 49,000 additional merges - were made in this assembly as compared with the 2.1 - assembly. -
- The whole genome shotgun data were derived primarily from - the donor Clint, a captive-born male chimpanzee from the - Yerkes Primate Research Center in Atlanta, GA, USA. - The sequence data were assembled and organized by the - Washington University Genome Center. The underlying whole - genome shotgun data were generated at the Washington - University School of Medicine and the Broad Institute. - For detailed information about the assembly - process, see the sequencing and analysis discussion in the - GenBank accession record. -
-- Bulk downloads of the sequence and annotation data are - available via the Genome Browser - FTP - server or the - Downloads - page. The complete set of sequence reads is available at the - - NCBI trace archive. These data have - specific - conditions for use.
-- We'd like to thank the International Chimpanzee - Sequencing and Analysis Consortium, Washington - University at St. Louis School of Medicine Genome Sequencing - Center, and the Broad Institute for providing this assembly. - We'd also like to acknowledge the UCSC team who worked on - this release: Hiram Clawson, Greg Roe, and Donna Karolchik. - The chimpanzee browser annotation tracks were generated by - UCSC and collaborators worldwide.
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19 January 2011 - Browser Released for Zebrafish Zv9 Assembly: The most recent zebrafish assembly -- Zv9 (UCSC version danRer7, Jul. 2010) -- is now available in the UCSC Genome Browser. - Read more. -
- 10 January 2011 - Introducing Genome Browser Right-click Navigation: - Several of the common display and navigation operations - offered on the Genome Browser tracks page may now be quickly - accessed by right-clicking on a feature on the tracks image - and selecting an option from the displayed menu. - Read more. -
- 2 December 2010 - -Searching for Tracks Just Got Easier!
- With our latest Genome Browser release, we've introduced a - new track search feature that will help you to quickly and - easily find and display specific annotation data sets. The - search feature is available via the "track search" button - on the browser gateway and tracks display pages. - Read more. - + Read more + + +==> News Archives +