(Photo courtesy of Steven Murray, CSU Fullerton)
|
|
|
Strongylocentrotus purpuratus (Photo courtesy of Steven Murray, CSU Fullerton) |
The Sep. 2006 Strongylocentrotus purpuratus draft assembly (Baylor release Spur_2.1) was produced by the Baylor College of Medicine's Human Genome Sequencing Center (BCM HGSC). For more information about this assembly, see Spur_v2.1 in the NCBI Assembly database.
A genome position can be specified by the accession number of a sequenced genomic region, an mRNA, a chromosome (or scaffold) coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the S. purpuratus genome. See the User's Guide for more information.
| Request: |
Genome Browser Response: |
|
| Scaffold12150 | Displays all 1,373,087 bases of Scaffold12150 | |
| Scaffold12150:1-10,000 | Displays first 10,000 bases of Scaffold12150 | |
| AF321312 | Searches for regions of genome aligning to mRNA with GenBank accession AF321312 | |
| tbp | Searches for regions of genome aligning to tbp gene | |
| cyclin dependent | Lists cyclin-dependent protein mRNAs | |
| davidson | Lists accessions deposited by authors named Davidson | |
| Wessel,G.M. | Lists mRNAs deposited by co-author G.M. Wessel | |
| Use this last format for author queries. Although GenBank requires the search format Wessel GM, internally it uses the format Wessel,G.M. | ||
The Sep. 2006 release of the purple sea urchin genome (Strongylocentrotus purpuratus) is now available in the UCSC Genome Browser. This assembly, UCSC version strPur2, was produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC) and corresponds to their Spur_2.1 assembly.
The Spur_2.1 release was assembled from BAC sequence reads (approximately 2x coverage) and whole genome shotgun reads (6x coverage), and utilizes BAC tiling path information. The BCM HGSC Atlas-2.0 genome assembly system was used to generate this assembly. The total length of all contigs greater than 1 kb is 804 Mbps. When the gaps between contigs in scaffolds are included, the total span of the assembly is 907 Mbps. The estimated size of the genome based on the assembly is 814 Mbps.
Compared to previous sea urchin releases, the Spur_2.1 assembly is more continuous and has fewer false duplications; contaminations identified in the previous Spur_2.0 assembly have been removed. This draft assembly may contain errors; therefore, users should exercise caution. Typical errors may include misassemblies of repeat sequences, collapses of repeat regions, and artificial duplications in polymorphic regions. However, base accuracy in contigs is usually very high with most errors near the ends of contigs.
More assembly details can be found in the Spur_2.1 README file and on the BCM HGSC Sea Urchin Genome Project web page.
Bulk downloads of the sequence and annotation data are available from the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The initial set of strPur2 annotation tracks was generated by UCSC. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.