The Drosophila yakuba Release 2.0 (Nov. 2005) draft genome sequence was produced by the Genome Sequencing Center at the Washington University (WUSTL) School of Medicine in St. Louis.

### Sample position queries

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:1-75000 |  | Displays first 75,000 bases of chromosome Yh (h = heterochromatin random reads)
AF532011 |  | Displays region aligning with D. yakuba mRNA with GenBank accession number AF532011
BQ705701 |  | Displays region aligning with D. yakuba EST with GenBank accession BQ705701
p53 |  | Lists mRNAs related to the p53 tumor suppressor
zinc finger |  | Lists zinc finger mRNAs
huntington |  | Lists mRNAs associated with Huntington's disease
Tautz,D. |  | Lists mRNAs deposited by co-author D. Tautz
Use this last format for author queries. Although GenBank requires the search format Tautz D, internally it uses the format Tautz,D..

### Assembly details

The Release 2.0 assembly includes both raw whole genome shotgun (WGS) data and data from two rounds of automated, directed read selection, which improved the sequence quality and narrowed or (in some cases) closed gaps. The raw WGS assembly data consists of 8,362 supercontigs larger than 1 kb, with a total size of approximately 161 Mb and an N50 length of about 2.5 Mb. The total number of contigs greater than 1 kb is 11,806, with a total size of approximately 161 Mb and an N50 length of 119 kb.

The data were intially assembled using the whole-genome assembly program, PCAP (Huang et al. (2003)). To create chromosomal assignments and ordering along the chromosomes, WUSTL first identified regions of the D. yakuba assembly that uniquely aligned with the D. melanogaster genome. The D. yakuba contigs were initially ordered by their position along the assigned D. melanogaster chromosomes (or segments for the heterochromatin). Alignment of all D. melanogaster mRNAs against the D. yakuba assembly were used to confirm these DNA-based alignments. WUSTL then introduced the inversions indicated by the D. yakuba sequence assembly to create the D. yakuba chromosomal files. The number of inversions required and the resulting banding patterns are in good agreement with the expected number and patterns, based on polytene chromosome banding data from Lemeunier and Ashburner (1976).

The sequence is distributed among the following chromosomes: 2L, 2R, 2h, 3L, 3R, 3h, 4, X, Xh, Yh, 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 or ChrNh_random.

For more information about the D. yakuba assembly and statistics, see the WUSTL Genome Sequencing Center Drosophila yakuba web page.

Downloads of the droYak2 data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page. The droYak2 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 this release.