(Photo courtesy of Genoscope)
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Tetraodon nigroviridis (Photo courtesy of Genoscope) |
The Tetraodon nigroviridis V7 assembly (February 2004) was provided by Genoscope, Evry, France. The assembly is the result of a collaboration between Genoscope and the Eli and Edythe L. Broad Institute of MIT and Harvard, MA, USA. The sequence data, which were assembled using the Arachne program, were generated by both institutes. The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute (NHGRI). For more information about this assembly, see ASM18073v1 in the NCBI Assembly database.
A genome position can be specified by the accession number of an mRNA or EST, a chromosome range, or keywords from the GenBank description of an mRNA. The following list provides examples of various types of position queries for the Tetraodon genome. Note that some position queries (e.g. "huntington") may return matches to the mRNA records of other species. In these cases, the mRNAs are mapped to their homologs in Tetraodon. See the User Guide for more information.
| Request: |
Genome Browser Response: | |
| chr1 | Displays all of chromosome 1 | |
| chr1:1-200000 | Displays first two hundred thousand bases of chromosome 1 | |
| chr1:100000+2000 | Displays a region of chromosome 1 that spans 2000 bases, starting with position 100000 | |
| CR731623 | Displays region containing Tetraodon mRNA with GenBank accession number CR731623 | |
| BU572495 | Displays region containing Tetraodon EST with GenBank accession BU572495 | |
| IL11 | Lists mRNAs related to IL11 (interleukin-11) | |
| pseudogene mRNA | Lists transcribed pseudogenes but not cDNAs, in GenBank | |
| T-cell receptor | Lists mRNAs for T-cell receptor genes in GenBank | |
| kinase | Lists many kinase mRNAs | |
| tyrosine kinase | Lists only tyrosine kinases | |
| breast cancer | Lists mRNAs associated with breast cancer | |
| abkevich | Lists mRNAs deposited by scientist named Abkevich | |
| Lutfalla,G. | Lists mRNAs deposited by co-author G. Lutfalla | |
| Use this last format for author queries. Although GenBank requires the search format Lutfalla G, internally it uses the format Lutfalla,G. | ||
This assembly was constructed using the whole genome shotgun (WGS) approach, resulting in a sequence coverage of about 7.9X. The assembly contains 45,609 contigs and 25,773 scaffolds generated by the Arachne program and covers more than 90% of the genome. Additional linking data were used to build ultracontigs and to organize the assembly into chromosomes. Genoscope estimates the size of the Tetraodon genome to be about 385 Mb.
Downloads of the Tetraodon data and annotations may be obtained from the UCSC FTP site or Downloads page. These data have been freely provided by Genoscope before publication for use in the UCSC Genome Browser with specific conditions for use.
Many thanks to Genoscope and the Broad Institute of MIT and Harvard for this genome assembly. The tetNig1 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.