The August 2003 Drosophila pseudoobscura genome assembly is based on the Freeze 1 assembly produced by the Human Genome Sequencing Center (HGSC) at Baylor School of Medicine.

Sample position queries

A genome position can be specified by a scaffold coordinate range, the accession number of an mRNA or RefSeq entry, a gene name, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the D. pseudoobscura 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 D. pseudoobscura. See the User's Guide for more information.

Request:
    Genome Browser Response:
Contig3128_Contig3153 Displays all of scaffold Contig3128_Contig3153
Contig53_Contig54:1-50,000 Displays first 50,000 bases of scaffold Contig53_Contig54

AF025805 Displays region of genome aligning to mRNA with GenBank accession AF025805
dock Displays region of genome aligning to gene with identifier dock (a D. melanogaster gene)
NM_057677 Displays region of genome aligning to RefSeq accession with identifier NM_057677 (a D. melanogaster RefSeq entry)

zinc finger Lists zinc finger mRNAs
kruppel zinc finger Lists only kruppel-like zinc fingers
huntington Lists candidate genes associated with Huntington's disease
zahler Lists mRNAs deposited by scientist named Zahler
Zeng,L.W. Lists mRNAs deposited by co-author L.W. Zeng

Use this last format for author queries. Although GenBank requires the search format Zeng LW, internally it uses the format Zeng,L.W.

Assembly details

Freeze 1 is a whole genome shotgun assembly produced using Baylor HGSC's assembly engine, Atlas. The assembly, which provides approximately 7x coverage of the euchromatic portion of the genome, contains 759 scaffolds. The scaffold N50 size is 1,018,646 bp. The total scaffold size for this assembly is 139.3 Mbp, with an average size of 184,465 bp. Due to an assembly error, four large scaffolds "jumped" chromosomes. These have been split into "A" and "B" parts in the downloadable assembly files: Baylor HGSC has provided a putative chromosome assignment for the majority of larger scaffolds (> 90% of unique sequence), based on conservation between the Muller elements.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data are made available with specific conditions for use. The dp2 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.

GenBank Pipeline Details

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