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A Database of Drosophila Genes & Genomes

Community Genomes Papers

November 7, 2006

Dear 12-Fly Genome Analysis community,

It is now the beginning of November and both the evolutionary analyses and conservation analyses have been moving forward. However, the shepherding of the annotations of 12 genomes at once has been quite a challenge, and it turned out that additional time was required to ensure the quality of the annotation sets that were produced through the efforts of several collaborative groups. Consequently, we are a couple of months behind our previously announced schedule. However, we are pleased to announce that we are now aiming for December 15 as our new target date for submission of two community papers for publication. With this date in mind we hope that you will consider both contributing to these core papers and timing the submission of any separate papers to synchronize with this Dec. 15th target. With the annotation issues behind us, we are confident that Dec. 15 is a firm date.

We would like to coordinate companion paper submissions as much as possible, as well as invite you to summarize selected highlights of your analyses for the community papers. These highlights in the community submissions can serve as pointers to individual companion papers.

We have grouped the comparative analyses into two main parts:

  • (1) An evolutionary paper, describing the sequence and annotation of each species, and the evolutionary changes among them, coordinated by Michael Eisen ( and Andy Clark ( [Word document]
  • (2) A conservation paper, describing how the 12 genomes help us to better understand the annotation of D. melanogaster, coordinated by Manolis Kellis ( [Word document]

We attach outlines of the two papers along with the responsible parties for various aspects of the analysis to be presented in each. If you have contributions in an area in which there is an assigned responsible party, we would still value additional contributions to these analyses. In some cases, there are topics with no assigned responsible party. We especially encourage members of the community to come forward if you have been carrying out analyses in these areas.

If you have selected highlights of your individual papers that you think would fit within either of the main papers, please contribute them by contacting Mike, Andy or Manolis. Contributions of such highlights will be recognized with co-authorship on the relevant paper.

Please notify us of any contributions that you intend to make ASAP, but no later than November 15 so that a revised outline can be circulated.

In a subsequent mailing, we will update you on the journals selected for the community papers and journals that are interested in hosting coordinated submissions timed to these core papers. We would also like to compile a list of planned parallel publications. We encourage you to forward these to Bill Gelbart ( or Thom Kaufman (

Finally, we wish to make some comments about data coordination. First, by the end of this week, a single page containing all reference data sets ( will be available by links from FlyBase and AAA. We urge all groups to use these reference data sets, including the GenBank scaffold accessions and coordinates in their publications. Lookup tables for the interconversion of the GenBank and CAF1 scaffold IDs and coordinates is available on the Datasets page. In addtion, there has been a strong group effort make a shared multi- alignment of protein coding genes, and using these will make analysis more accurate, robust (and faster and easier) and will facilitate cross-comparisons of the contributing groups' results.

Thank you in advance for your consideration and your willingness to coordinate with this revised schedule.


The AAA coordinating committee for the 12 Drosophila species