What is Arm U in Drosophila melanogaster?

Arm U is an unordered assembly of unplaced sequence scaffolds. More information about Arm U can be found in the GenBank record (FA000001).

Here is the comment section from this record:
This record is an unordered assembly of unplaced (chrUn) sequence scaffolds that lie in heterochromatic regions of the genome, and does not reflect the structure of a biological molecule. Intervals between scaffolds are denoted by 100 N's, and the order and orientation of the scaffolds with respect to one another is not known. Scaffolds joined in this record either cannot be localized to a particular chromosome or have conflicting localization data. It is provided for the FlyBase Consortium as an aid for sequence tracking. For further information about this sequence, please visit our Web site (http://www.dhgp.org). WARNING: The order and orientation of scaffolds in this record are unknown.

Where can I find information on Drosophila Gold Collection clones?

If there is a full length DGC clone associated with a gene you will find it in the gene report under the REAGENTS/cDNA section in its own field. For example: Dmel\lark lists LD40792 as a DGC clone.

If the "DGC cDNAs" field does not appear in a report it means that a DGC clone has not been identified for the gene.

Do you provide decorated FASTA sequences for gene ... ?

This works for some genes but not others. A work around for this until we get it fixed is to use the GBrowse 'Download sequence ' option. Here's how it works:

Using Dlic2 (CG1938) as an example, copy the coordinates from the 'Physical map' field of the annotation report into the GBrowse 'Find Genome Region' window. This displays X:10999619..11008430 in GBrowse. In the 'Feature Tracks' panel select the features you're interested in and update the map. Then open the 'Download sequences' panel toward the bottom of the page. From the 'Dumps,...' menu select 'Dump Decorated FASTA file' and choose 'Configure'. Select display settings to distinguish the features you're interested in.

How can I obtain flanking gene sequence?

Unfortunately there is not an easy way to get the flanking sequences for a specific subset of genes in FlyBase. You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end from the ftp site.

The file: dmel-all-gene_extended2000-r4.2.1.fasta contains these sequences. There is also a file with all intergenic sequences.

You would then need to identify your genes of interest and pull out the section of sequence you were interested in.

How can I obtain an Exelixis Clone?

Unfortunately Exelixis made the decision not to save their libraries as they felt the clones were largely overlapping with existing ones. Obviously that is not truly the case but that is the situation so none of these clones are available.

How do I cite the Drosophila phylogeny?

The Drosophila phylogeny shown on FlyBase is a compilation of information that can be found in:

How can I search the abstracts of the Annual Drosophila Research Conference?

The Annual Drosophila Research Conference is a meeting of the Genetics Society of America, so you can reach abstracts from the Drosophila meetings (back to 2000) on the GSA website:

From this, you can go to the abstract search page to find your abstract-of-interest, for example:

http://www.drosophila-conf.org/genetics/dros06/dros06s/