News and Announcements
|New GBrowse feature ... May 2007|
Gene summaries and information on transgenic insertions
We have introduced pop-ups into GBrowse to provide you with a gene summary when you place your mouse over a gene span, and information on an insertion when you hover over the transgene insertion site.
These features are available for the D. melanogaster genome and the "Insertions in Stock Collections" data.
In the GBrowse view of the D. pseudoobscura genome mousing over a gene span also produces a pop-up with information on the gene. However, we do not provide information about the GLEANR high confidence prediction sets in the other genomes, but you can obtain information about the putative D. melanogaster ortholog by hovering over the ortholog track if an orthology call has been made.
We hope you find the pop-ups useful and welcome your feedback.
|Summaries and in situ images ... May 2007|
FlyBase is introducing two major changes to the the gene report pages.
In situ images
In a collaboration with FlyExpress we are including in situ images in the FlyBase gene reports. These images, which originate from the BDGP gene expression project, are located under the "EXPRESSION DATA" section of the "GENE PRODUCTS & EXPRESSION" part of the report page. If you click on one of the images you are taken to a FlyExpress page showing in situ images of the gene for that particular stage of embryonic development. If you would like to see all the FlyExpress in situ images of the gene, or search for similar patterns, you can click on the link at the bottom of the section.
Gene summaries return
Many respondents to the FlyBase User Survey requested the return of gene summaries. Summaries that provide an overview of selected classes of gene information have now been incorporated into FlyBase gene reports. Like the previous gene summaries, the new summaries are automatically generated, but using a different algorithm that better represents the range of information in a selected class. The included categories are: gene identifiers, map location, molecular function, biological process, number of alleles and their phenotypes, and numbers of transcripts and proteins. A file of the summaries can be downloaded from the Precomputed Files page. We hope you find these summaries useful and welcome your feedback.
|Profile Manager released ... Feb 2007|
FlyBase has released a new feature for our collapsible reports called Profile Manager. The Profile Manager lets you configure the open and closed state of sections on a report page and save the configuration to a named profile. Here is a list of things you can do with the Profile Manager:
|New Species BLAST & GBrowse ... Aug 2006|
FlyBase is pleased to announce that we have developed a new interface for the community to query and view assembled and annotated versions of 11 of the sequenced Drosophila species:
D. anannassae, D. erecta. D. grimshawi, D. melanogaster, D. mojavensis, D. persimilis, D. pseudoobscura, D. sechellia, D. virilis, D. willistoni and D. yakuba.
You can access the 11 species from either the FlyBase BLAST page
or through the GBrowse window.
We have also provided a direct link between BLAST output and the GBrowse representation of the various species genomes and the relevant gene models/hit sites in the genome.
You will see that there are multiple tracks available on GBrowse for the newly represented species and these reflect the various annotation/gene model predictions from the labs that have provided each analysis (these can be clicked on or off as you wish) as well as GLEAN consensus sets of high confidence and those with lesser support called the "Exploratory Set". The GLEAN sets are provided as the default offering/response. We are also presenting a set of ortholog predictions computed in Mike Eisen's lab by Venky Iyer. These too appear as default. It is through these latter predictions that we offer a way to query the genomes from the GBrowse window. Simply choose your species from the <Data Source> pull down menu and wait a few seconds for GBrowse to go to that genome. Once there, type the Dmel gene symbol or CG##### of your choice into the <Landmark or Region> box and hit <Search>. If an ortholog has been predicted you will be taken to its position in the genome. If there is no predicted ortholog you will see a red-letter response <The landmark named XXX is not recognized. See the help pages for suggestions.> at the top of the page telling you this fact.
A second way into the genomes is through the new BLAST. Pick a gene and recover a FASTA file of its sequence. Copy and Paste said sequence into the BLAST window and start the query. Pick as many Drosophila species as you wish. When your query is returned you will see the standard list of hits. Pick one of the top hits and go to its specific record/alignment. You will note that there is an html link on the Score line that reads "BLAST HIT on Genome Map". Click on this link and you will be taken to the position on the appropriate species genome wherein the hit resides. The position of the hit will be highlighted in grey and this highlight will extend over as many of the evidence tracks as are open. The best hits should take you to the ortholog of your gene if there is one. The lesser hits can take you to places in the genomes of the various species that are the residence of small bits of sequence similarity but not orthology
Please be aware that these predictions are at this point preliminary and do not represent an official community consensus set of gene models. We have released this preliminary set of analyses so that the community can have a look at what is there in the available genomes and begin some of their own forays into the wealth of data that are now available from the community genome sequencing projects.
FlyBase wishes to thank all of those who have contributed to the analyses to this point and to especially thank the NIH and the NIGRI for providing support for this project.
Please have a look and get back to us with problems or suggestions.
The FlyBase Consortium.
|Insertions in GBrowse ... Aug 2006|
Transgene Insertions in Stock Collections has been added as a new option in FlyBase GBrowse.
Sequence-mapped insertions at the three major D. melanogaster stock centers -- Bloomington, Szeged, Kyoto -- and the Exelixis insertion collection distributed by the Artavanis-Tsakonis lab at Harvard Medical School can be displayed in individual tracks along with a subset of gene-related track options.
The URL http://flybase.org/cgi-bin/gbrowse/dmelstocks/ goes directly to this GBrowse view. From any other GBrowse view, select Insertions in Stock Collection as the Data Source. Use the Tracks panel to select the features you want displayed.
|Dmel r5 BLAST preview ... May 2006|
The BDGP and DHGP has released a new assembly of Drosophila melanogaster called Release_5. Release_5 is a single comprehensive assembly of the entire genome (both euchromatin and heterochromatin). This new assembly has several important features, most notably additional high quality assembled heterochromatin on the major chromosome arms and high quality assembled heterochromatin segments mapped to the base of the arms but not attached to the major arm assemblies.
FlyBase and the DHGP are in the process of migrating our gene annotations onto Release_5. We anticipate that the first annotation set on Release_5, called version Release_5.1, will be available on FlyBase and in GenBank in August 2006.
Until then, we are adding the unannotated Release_5 melanogaster genome to our set of genome BLAST databases. The default for melanogaster will remain the Release_4 arms plus the Release_3.2b heterochromatin, until Release_5.1 becomes available.
|New Synteny Table ... Apr 2006|
In anticipation of the publication of the results of the community and individual comparative analyses of the genomes of 12 species of genus Drosophila, FlyBase is providing this table that will allow our users to easily view the syntenic relationships among the arms of the 12 sequenced genomes ....
|FlyBase QueryBuilder ... Feb 2006|
QueryBuilder is a new search tool that provides one-stop shopping for information in FlyBase.
|Apollo Support ... Sept 2006|
From this point forward FlyBase will be providing Apollo viewable annotation data in chado-xml format only. The latest version of Apollo has been modified to retrieve annotation data via the web in this format. Therefore, we recommend that you upgrade to the latest available version of Apollo
We will no longer provide annotation data in GAME-XML format and while Apollo is still able to load and view existing GAME-XML data the data files must be available on the local machine as web retrieval of GAME files is no longer supported.
Please be aware that when Apollo is retrieving annotation data from the web it is obtaining precomputed chunks of xml. While the pieces have been generated to not span any gene models retrieval by sequence range may not result in the exact sequence requested being loaded into Apollo.
Please use the contact FlyBase form to send questions and requests for help to FlyBase.
|Linkouts in FlyBase ... Mar 2006|
FlyBase offers direct "linkouts" from our gene report pages to other web-based Drosophila data services. . The FlyBase Consortium wishes to thank the organizers and developers of these data sets for helping us provide a great deal of valuable information on Drosophila genes and genomes.
In addition to these links FlyBase also provide direct links to the Drosophila records in the major international nucleotide, protein and bibliographic databases.
|COMMUNITY NEWS & ANNOUNCEMENTS|
|Degree in Genetics and Molecular Biology honoris causa Awarded to Dan L. Lindsley ... June 2007|
On behalf of our Drosophila colleagues at the University of Rome, FlyBase is delighted to announce that on July 2nd 2007 the University of Rome "La Sapienza" will confer on Dan L. Lindsley a degree in Genetics and Molecular Biology honoris causa. The ceremony will take place in the Aula Magna of "La Sapienza" at 10:30 am.
As many of you know Dan's tireless efforts in the production of the Red Books laid the ground-work for what you now see on the www as FlyBase. However Dan's contributions go well beyond this community effort and include seminal contributions to the field of chromosome mechanics and our understanding of the genetic regulation of meiosis and male fertility to name but three.
We at FlyBase offer Dan our heartfelt congratulations on this very well deserved honor.
|Tucson Drosophila Stock Center - new international rates ... May 2007|
The Tucson Stock center has announced a change in its rates for International customers.
|12 genomes - update ... Mar 2007|
Dear Drosophila Genome Colleagues,
This is an update on the status of the submissions of the main manuscripts on the initial analyses of the 12 Drosophila genomes. Though there has been unavoidable slippage due to the complexities of handling all of this genomic data at once, the manuscript preparation is in its final phase and the manuscripts are targeted for submission by mid-March.
If you have a companion paper that you have submitted, the lead authors of the two papers (Manolis Kellis, conservation paper; Michael Eisen and Andy Clark, evolution paper) request that you send them the Author, Title and Journal information for cross-referencing for our submissions and, if possible, a pdf of the submitted manuscript.
Their email address are:
Thank you for continuing input in bringing this challenging project to a successful conclusion.
The 12 Genomes Coordinating Committee
|12 genomes - publication plans ... Dec 2006|
This is a follow-up to our mid-November announcement on publication plans for the main and companion papers on initial analyses of the 12 sequenced Drosophila genomes.
Each of these journals has an excellent track record in reaching its target audience and is planning a special section devoted to the 12 Drosophila Genomes papers. Timing of publication will be coordinated amongst all of these journals. All papers will be Open Access.
Please note that these journal recommendations are simply that ... recommendations. We feel that there will be more impact with several publications in a focused set of journals, and special sections devoted to the 12 genome papers. This also makes it easier to coordinate with the publication of the main articles. We are anticipating at least 40 companion papers by the target submission date, based on emails we have received. If you have not contacted us yet, and are planning a companion paper, please do so as soon as possible.
When submitting to one of the recommended journals, please indicate in your cover letter to the editor that you wish your paper to be reviewed as part of the "12 Drosophila Genomes" special section, to ensure that it receives the necessary expedited review and is part of the coordination process amongst the designated journals.
Please let us know in advance which journals you will be submitting your companion papers to, even if they are not in the recommendations above, so that both we and the editors know what to expect. Send that information, as well as any questions you have, to the following members of the AAA coordinating committee:
The AAA Coordinating Committee
|Tucson Drosophila Stock Center - new prices ... Dec 2006|
Tucson Drosophila Stock Center price increase announcement.
|Community Genomes Papers ... Nov 2006|
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:
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 (gelbartmorgan.harvard.edu) or Thom Kaufman (kaufmanbio.indiana.edu).
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 (http://rana.lbl.gov/drosophila/wiki/index.php/Datasets) 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
|Fly - A new journal ... Sep 2006|
Fly is a new journal that will focus exclusively on Drosophila research
|Off-Target Effects: DRSC ... Sep 2006|
off-targets in Drosophila RNAi screens announcement.
|Ed Novitski Obituary ... Aug 2006|
"With great sadness FlyBase wishes to announce the passing of
on June 29 of this year. Ed was an important figure as a
Drosophila geneticist, particularly in the understanding of the
meiotic behavior of complex chromosomal rearrangements. We
extend our sympathies to his family and to his many colleagues
and former students."
|New Fly-Till Service ... May 2006|
FLY-TILL SERVICE FOR CHROMOSOME 2
The Seattle TILLING Project (STP) is announcing the opening of the Fly-TILL service for chromosome 2. TILLING (Targeting Induced Local Lesions IN Genomes) is a general reverse genetic technique that can deliver allelic series of EMS-induced point mutations in target regions of approximately 1.5 kb. STP has been operating a Fly-TILL service using the Zuker chromosome 3 lines since March of 2005, and has discovered over 800 mutations in 65 gene targets. The average time to complete an order has been 11 weeks. Tests with 3000 of the Zuker chromosome 2 lines suggest a mutation density and data quality similar to that obtained with chromosome 3.
To celebrate the opening of our new service, we are offering for a limited time 50% off on all Fly-TILL orders (either Chromosome 2 and 3). We will screen 3000 lines for $1400 and for $2500 we will screen our entire population (about 6000 Chromosome 3 lines, or 5600 Chromosome 2 lines). We have a maximum number of orders that we will accept at this price. Hurry while supplies last! You can place your order at:
Thank you for your interest and support.
Bradley J. Till
|Status of Species Genomes ... May 2006|
May 10, 2006
We are writing to bring you up to datewith a status report of the comparative Drosophila genome sequencing and analysis plans.
Sequencing and Assembly
Sequencing & Assembly Status
U. MD. Reconciled Arachne/Celera Assembly
U. MD. Reconciled Arachne/Celera Assembly
U. MD. Reconciled Arachne/Celera Assembly
U. MD. Reconciled Arachne/Celera Assembly
U. MD. Reconciled Arachne/Celera Assembly
U. MD. Reconciled Arachne/Celera Assembly
Mosaic PCAP Assembly
Most species have been sequenced to deep WGS coverage levels. The persimilis and sechellia projects have been sequenced to low WGS coverage (~3-4X) with the core assemblies derived independently and then enhanced by synteny to related species. For simulans, there is 2.8X coverage of one strain (w501) and 1X coverage of 6 other strains. The mosaic simulans assembly layers reads from these other strains onto the core w501 assembly.
For Drosophila melanogaster, the finished Release_4 arms (BDGP) and draft Release_3.2b heterochromatin (DHGP) will be used as the reference assembly. For Drosophila pseudoobscura, the Release_2 Atlas Assembly (Baylor) will be the reference assembly.
Timetables for Submissions of Annotation Sets
Downstream Analyses & Initial Publications
Mapping Supercontigs onto the Chromosome Arms
Whole Genome Alignments Our discussions with alignment groups led us to conclude that it does not make sense to strive for a single set of DNA based alignments because they all differ somewhat, and people have their own preferences about which ones are most useful for their particular downstream analyses. We would, however, like to make sure that we end up with alignments of a similar quality as those being produced for the human ENCODE regions. As it stands now, it looks as though we will end up with four different sets of alignments: MERCATOR/MAVID (Pachter), Multiz (UCSC), LAGAN (Sidow/Batzoglou) and TBA (Webb Miller/Karro).
While we do not wish to constrain any other groups work in any other area of research on these Drosophila genomes, we are happy to invite others to contribute work that might be appropriate for the main paper on the assembly, annotation and analysis of these species. Please contact Doug Smith (firstname.lastname@example.org), Bill Gelbart (email@example.com) or Thom Kaufman (firstname.lastname@example.org) regarding any such contributions.
Accessing Drosophila Genome Resources
Doug Smith, Agencourt Inc. (email@example.com)
|DROSOPHILA NETWORK NEWS (BIONET.DROSOPHILA)|