Photo courtesy of Michael Fuentes and Héctor Escrivà, Observatoire Océanologique de Banyuls sur mer. All rights reserved.
|
|
|
Branchiostoma lanceolatum Photo courtesy of Michael Fuentes and Héctor Escrivà, Observatoire Océanologique de Banyuls sur mer. All rights reserved. |
The Mar. 2006 Branchiostoma floridae draft assembly (JGI v.1.0 (March 2006)) was produced by the Joint Genome Institute.
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 Lancelet genome. See the User's Guide for more information.
| Request: | Genome Browser Response: | |
|---|---|---|
| chrM | Displays all of chromosome M | |
| chrUn:1-1000000 | Displays first million bases of chr Un | |
| chrUn:1000000+2000 | Displays a region of chr Un that spans 2000 bases, starting with position 1000000 | |
| | ||
| AF303216 | Displays region of mRNA with GenBank accession number AF303216 | |
| AI391435 | Displays region of EST with GenBank accession AI391435 | |
| | ||
| pseudogene | Lists transcribed pseudogenes | |
| 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.. | ||
The genome of Branchiostoma floridae is estimated to be approximately 575 Mb contained in 19 pairs of chromosomes, and is being sequenced to approximately 8.1 X depth.
v.1.0 (March 2006): Approximately 6.5 Million shotgun reads were initially assembled using JAZZ. A high allelic polymorphism rate of 5-10% allowed the two haplotypes to be assembled separately at approximately 75% of genomic loci. There are a total of 3,032 scaffolds, with a total length of 923 Mb composed of 81,073 contigs. Half of the assembly is contained in 174 scaffolds, all at least 1.6 Mb in length. The length-weighted mean contig size (L50) is 26 kb.
The lancelet mitochondrial sequence is also available as the virtual chromosome "chrM". (GenBank: NC_000834.1 GI:5881414)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 Lancelet 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.