The Drosophila Genome Project at the HGSC has transitioned to sequencing the euchromatic portion of the Drosophila pseudoobscura genome using a comparative sequence approach. This project builds on the successful collaborative effort with Dr. Gerald Rubin's Berkeley Drosophila Genome Project (BDGP) and Celera Genomics to map and sequence the euchromatic portion of the Drosophila melanogaster genome. The Drosophila Genome Project is funded by the National Human Genome Research Institute, National Cancer Institute, and Howard Hughes Medical Institute.

The BCM-HGSC collaborated in the generation of a D. melanogaster BAC-based physical map by fingerprinting and assembling approximately 10,000 random Drosophila BAC clones. Integration of the fingerprint data with the BDGP generated STS content map and in situ hybridization produced an essentially complete map of the euchromatic genome (Science Mar 24 2000: 2271-2274). Fingerprinting of the minimal tiling path clones with two additional restriction enzymes generated a quality control dataset for final BAC clone assembly.

Through the efforts of the Drosophila Genome Project, 120,000 kb of Euchromatic Drosophila melanogaster sequence was produced worldwide (Science Mar 24 2000: 2194) with 1063 gaps remaining on 3L and X to be finished. Gaps in this context refers to the number of gaps in the Celera Unitigs prior to the surrogate repeat consensus sequence insertion in the published sequence. Chromosome arms 3L and X had 238 and 172 surrogate insertions, respectively. Effort at Baylor HGSC is directed at finishing chromosome arms 3L and X.

A summary overview of each chromosome arm is available through the Tiling Path View where the relative position and state (finished, redundant) of each BAC is presented. A list of the ordered contigs with links to the BACs included is provided by the BAC Status Report. A report on the current state of the finishing efforts is available in the Gap Status Report.

Individual BAC clones can be searched using the Sequencing Project Browser with a query of:

• an Accession number (AC023706)
• a Clone name (RP98-4D11)
• or a Project name (DRIU)

in the appropriate query box. Sequences can be retrieved from NCBI or the BCM HGSC FTP site using links in the output.

Using the BCM HGSC project name, richer views of the data are provided by :

• Contig View - comparison of the Celera and Phrap assemblies of a project.
• Gap View - statistics and a visual image of the Gaps within a project.
• FTP site - access to fasta and quality files.

More information about the state of the sequence surrounding a particular Gap, including the position and pairing of individual sequencing reads can be found using the Sequence Read View.

There are two types of BLAST searches available.

• Flybase BLAST - Searches all Drosophila reads and provides links to the individual matched sequences through the NCBI.
• Baylor BLAST - Searches only Baylor Drosophila reads and provides links to the Individual matched sequences through the BCM FTP site.

Fingerprint assemblies are available as gif files and as raw data on the FTP site for use with FPC. STS content maps are available for 3L and X.

Clones are available from BACPAC resources.

International Genome Consortium Database

Conditions for use