Tetraodon assembly and gene annotation
Assembly
The Tetraodon genome project is a collaboration between Genoscope and the Broad Institute (MIT). This Ensembl website presents sequence data and analyses provided by the two institutes.
The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute.
The genome assembly was performed using Arachne (Jaffe D.B. et. al. 2003. Gen. Res. 13, 91-96). This site presents version 7 of the assembly.
Gene annotation
Genes were annotated by Genoscope, combining evidence from Geneid, Genscan, Genewise and Exofish predictions with alignments of Tetraodon cDNAs to the genome. This was done automatically using GAZE (Howe K., Chothia T. and Durbin R. 2002. Gen. Res. 12, 1418-27) with a custom-designed configuration and gene structure model.
The annotation also includes 87 manually curated structures of a number of HOX and Cytokine genes.
More information
General information about this species can be found in Wikipedia.
Statistics
Summary
| Assembly | TETRAODON 8.0, Mar 2007 |
| Base Pairs | 358,618,246 |
| Golden Path Length | 358,618,246 |
| Annotation provider | Ensembl |
| Annotation method | Full genebuild |
| Genebuild started | Nov 2007 |
| Genebuild released | Jul 2008 |
| Genebuild last updated/patched | May 2010 |
| Database version | 113.8 |
Gene counts
| Coding genes | 19,602 |
| Non coding genes | 813 |
| Small non coding genes | 806 |
| Misc non coding genes | 7 |
| Pseudogenes | 147 |
| Gene transcripts | 24,078 |
Other
| GSC gene prediction | 24,558 |
| Genscan gene predictions | 23,832 |
| Short Variants | 911,017 |