FRT Deletion Hunter - Incorporating DrosDel and Exelixis element data

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Please note that the FDD deletions are a guide for constructing deficiencies in areas of interest and are not being actively made by DrosDel. They are therefore not available for ordering.

In addition to our DrosDel collection, the PiggyBac elements made by Exelixis (Parks et al, 2004) have also been used to generate deletions by FRT-mediated recombination. While the collections are based on different transposable elements, they nevertheless contain very similar FRT sites. Therefore, in principal it may be possible to combine elements from each collection to increase the coverage of the genome and facilitate generation of highly-specific single gene deletions.
We therefore calculated all possible deletions smaller than 500kb that can be made by combining elements from the two collections and have named these FDDs (FRT-derived deletions).
To achieve this we used the sequence data from the Exelixis collection of insertions (available from Harvard Medical School to re-map these insertions with respect to the Release 5.1 genome sequence. Due to descrepencies on some lines between the Harvard sequence data and FlyBase, please check in FlyBase that the elements are still located where they are indicated. This problem will be fixed when any updated lists become available.

Combining both collections we find that a total, 534,209 FDDs can theoretically be constructed and that over 73,000 of these can be easily tracked through a change in eye colour. The remaining 460,625 deletions can be detected by specific PCR assay.

Exelixis stocks can be ordered from Harvard Medical School or Bloomington. Drosdel RS elements can be ordered from the Szeged Stock Centre via the DrosDel web site.

Parks A.L., Cook K.R., et al. Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome. 2004. Nature Genetics 36(3):288-292