The Drosophila simulans Release 1.0 (Apr. 2005) draft genome sequence was produced by the Genome Sequencing Center at the Washington University in St. Louis (WUSTL) School of Medicine.
A genome position can be specified by the accession number of an mRNA or EST, a chromosomal range, or keywords from the GenBank description of an mRNA. The following list provides examples of valid position queries for the Drosophila 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 Drosophila. See the User's Guide for more information.
| Request: |
Genome Browser Response: |
|
| chr2L | Displays all of chromosome 2L (see the Assembly Details section for a list of chromosomes present in this assembly) | |
| chrYh_random:1-75000 | Displays first 75,000 bases of chromosome Yh_random (h = heterochromatin random reads) | |
| AY017266 | Displays region aligning with D. simulans mRNA with GenBank accession number AY017266 | |
| BG642296 | Displays region aligning with D. simulans EST with GenBank accession BG642296 | |
| p53 | Lists mRNAs related to the p53 tumor suppressor | |
| zinc finger | Lists zinc finger mRNAs | |
| huntington | Lists mRNAs associated with Huntington's disease | |
| Panelli,S. | Lists mRNAs deposited by co-author S. Panelli | |
| Use this last format for author queries. Although GenBank requires the search format Panelli S, internally it uses the format Panelli,S.. | ||
The Release 1.0 D. simulans assembly represents a mosaic of several different D. simulans lines. The assembly process began with an ~4X WGS assembly of the the D. simulans w501 line. The w501 contigs were initially anchored, ordered and oriented by alignment with the D. melanogaster genome. The assembly was then examined for places where the w501 assembly suggested inversions with respect to the D. melanogaster assembly. One major inversion was found, confirming the already documented inversion found by Lemeunier and Ashburner (1976). Six other D. simulans lines (c167.4, md106ts, md199s, nc48s, sim4, and sim6) were assembled with ~1X coverage. Using the 4X WGS assembly of the simulans w501 genome as a scaffold, contigs and unplaced reads from the 1X assemblies of the other individual D. simulans lines were used to cover gaps in the w501 assembly where possible. Thus the resulting assembly is a mosaic containing the w501 contigs as the primary scaffolding, with contigs and unplaced reads from the other lines filling gaps in the w501 assembly.
Mitochondrial sequence was downloaded separately from GenBank. Total size, excluding the gapless 14,972 bp mitochondrial sequence, is 142,405,747 bp including gaps and 127,241,461 bp excluding gaps.
The sequence is distributed among the following chromosomes: 2L, 2R, 2h (random only), 3L, 3R, 3h (random only), 4, X, Xh (random only), Yh (random only), M (mitochondria) and U. Sequence that could not be reliably ordered within a chromosome N has been placed on chrN_random. Heterochromatin that has been localized to a specific chromosome can be found in chrNh_random. For more information about the D. simulans assembly and statistics, see the WUSTL Genome Sequencing Center Drosophila simulans web page.
Downloads of the droSim1 data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page. The droSim1 annotation tracks were generated by UCSC and collaborators worldwide. Thanks to the Genome Sequencing Center, WUSTL School of Medicine for providing the sequence of this genome. See the Credits page for a detailed list of the organizations and individuals who contributed to the success of this release.