Gasterosteus aculeatus
Credit: Jeffrey S. McKinnon, East Carolina University All rights reserved. Photo courtesy of National Science Foundation.

The Feb. 2006 draft assembly of Gasterosteus aculeatus (Broad Institute v1.0) was produced by the Broad Institute at MIT and Harvard. For more information about this assembly, see ASM18067v1 in the NCBI Assembly database.

Sample position queries

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 stickleback genome. See the User's Guide for more information.

Request:   Genome Browser Response:
chrXIV   Displays all of chromosome XIV
chrIII:1-1000000   Displays first million bases of chr III
chrIII:1000000+2000 Displays a region of chr III that spans 2000 bases, starting with position 1000000
BT027921   Displays region of mRNA with GenBank accession number BT027921
CD500209   Displays region of EST with GenBank accession CD500209
mhc   Lists MHC mRNAs
mathias   Lists mRNAs deposited by scientist named Mathias
Kingsley,D.M.   Lists mRNAs deposited by co-author D.M. Kingsley
Use this last format for author queries. Although GenBank requires the search format Kingsley DM, internally it uses the format Kingsley,D.M..

Assembly details

The v1.0 stickleback genome has been sequenced to approximately 6X coverage. An estimated 87% of the sequence has been anchored to chromosomes (chrI - chrXXI). Of the remaining unanchored scaffolds, those that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn" with 1000 bp gaps between scaffolds. The stickleback mitochondrial sequence is also available as the virtual chromosome "chrM".

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 stickleback 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 this release.

GenBank Pipeline Details

For the purposes of the GenBank alignment pipeline, this assembly is considered to be: well-ordered.