Photo courtesy of Mansi Srivastava (CIG UC Berkeley)
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Nematostella vectensis Photo courtesy of Mansi Srivastava (CIG UC Berkeley) |
The Jun. 2007 Nematostella vectensis draft assembly is based on sequence version Nemve1 assembled and sequenced by the US DOE Joint Genome Institute(JGI).
A genome position can be specified by the accession number of a sequenced genomic region, an mRNA or EST, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the Starlet sea anemone genome. See the User's Guide for more information.
| Request: | Genome Browser Response: | |
|---|---|---|
| scaffold10 | Displays all of scaffold10 | |
| scaffold3:1-1000000 | Displays first million bases of scaffold 3 | |
| scaffold3:1000000+2000 | Displays a region of scaffold 3 that spans 2000 bases, starting with position 1000000 | |
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| BX950328 | Displays region of mRNA with GenBank accession number BX950328 | |
| BU335953 | Displays region of EST with GenBank accession BU335953 on scaffold 3 | |
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| pseudogene mRNA | Lists transcribed pseudogenes, but not cDNAs | |
| homeobox caudal | Lists mRNAs for caudal homeobox genes | |
| zinc finger | Lists many zinc finger mRNAs | |
| kruppel zinc finger | Lists only kruppel-like zinc fingers | |
| zhang | Lists mRNAs deposited by scientist named Zhang | |
| Taguchi,T. | Lists mRNAs deposited by co-author T. Taguchi | |
| Use this last format for author queries. Although GenBank requires the search format Taguchi T, internally it uses the format Taguchi,T.. | ||
Nematostella vectensis genome assembly 1.0 constructed with the JGI assembler, Jazz, includes approximately 7.8X WGS in small insert end-sequence coverage. After trimming for vector and quality, and excluding short/redundant scaffolds, there were 10,942 assembled scaffolds, containing 2,817,779 reads, and 357 Mbp of sequence. Further exclusion of contaminant and mis-assembled scaffolds reduced this to 10,804 scaffolds, with a total length of 356 Mbp. Roughly half of the genome is contained in 181 scaffolds all at least 473 Kb in length (N50).
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 genome assembly was presented in:
Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS. (2007) Sea anemone genome reveals ancestral eumetazoan gener epertoire and genomic organization. Science. 317, 86-94.
The Starlet sea anemone 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 the success of this release.