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).

Sample position queries

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.

  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.

Assembly details

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.