over the past 2 years , flybase has effected a complete migration and integration of its underlying databases into a postgresql chado genome database [ ( 1 ) , ] .
this has enabled a reimplementation from the ground up of the flybase public interface , with a complete redesign of the web pages , queries and reports ( figure 1 ) .
so , if you do not recognize us  take a second look ! detailed descriptions of the new flybase website will appear elsewhere . a flybase gene report .
the new flybase design allows the user to choose which sections and subsections to view . in this example , the table showing classical alleles has been opened .
flybase is an integrated resource for a vast array of genetic and molecular data concerning the drosophilidae , including interactive genomic maps , gene product descriptions , mutant allele phenotypes , genetic interactions , expression patterns , transgenic constructs and insertions of transgenic constructs , anatomy and images , and genetic stock collections ( 2 ) .
data are captured from bulk data sources , by curation from the literature , and by annotation based on assessment of contributing evidence ; data capture is organized around consistent attribution to primary sources . as far as possible , descriptive data are curated using controlled vocabularies ( cv ) , including the gene ontology for molecular function , biological process and cellular component ( 3 ) , the sequence ontology for sequence features ( 4 ) and an extensive cv for anatomical terms and developmental stages ( available as part of the open biomedical ontologies project , ) . although flybase has since its inception curated genetic and genomic information on the family drosophilidae , it is only with the recent whole - genome shotgun ( wgs ) sequencing and assembly of 11 additional species that substantial amounts of non - melanogaster data have appeared in flybase . indeed , it will be interesting to see how the availability of these wgs sequence assemblies will affect drosophila research through the ability to perform genome - wide comparative analyses at the sequence , phenotypic and biological process levels .
the species and their phylogeny are shown in the left - hand side of figure 2 . for the genome of the primary biological research species , drosophila melanogaster
, the euchromatic arms have now been finished to high quality by the bdgp [ ( 5 ) , ] . in the current release of the d.melanogaster genome assembly ( release 5 ;
see table 1 and ) , the arms include several megabases of centric heterochromatin as well as the entirety of the euchromatin .
the heterochromatin , sequenced by the bdgp and the drosophila heterochromatin genome project ( dhgp ) ( 6 ) , also includes several major scaffolds that are currently unattached to the arms .
the fully annotated arms are available from flybase and genbank ; the dhgp - annotated heterochromatic scaffolds should be contributed to flybase and genbank in late 2006 . the muller element arm synteny table .
the phylogenetic relationships of the 12 sequenced species are shown to the left , color - coded diagrammatic karyotypes and a table of syntenic relationships are shown to the right .
there is not a simple one - to - one correspondence of arms to muller elements for all of the species , due to fusion and inversion events relative to d.melanogaster in five of the species .
release 5 of the d.melanogaster genome assembly the other 11 species have all been sequenced in nhgri - funded large - scale sequencing centers ( table 2 ) , following the approval of three separate community - based white papers . the first white paper [ ( 7 ) ,  
proposed the sequencing of a second species , drosophila pseudoobscura , to support the annotation of d.melanogaster ( 8) . the second white paper [ ( 9 ) , ] proposed the sequencing of several isolates of drosophila simulans , a close relative of d.melanogaster , to understand the basis of variation within and between species , and the sequencing of a somewhat more distant member of the same species group , drosophila yakuba , as an outgroup .
the third white paper [ ( 10 ) , ] proposed the sequencing of eight additional species .
six of these species ( drosophila ananassae , drosophila erecta , drosophila grimshawi , drosophila mojavensis , drosophila virilis and drosophila willistoni ) were proposed principally to provide additional branch length for comparative genomic analysis in support of the annotation of d.melanogaster , as well as for the study of gene and chromosome evolution on a whole - genome scale .
the other two species , d.persimilis and d.sechellia , are sibling species of d.pseudoobscura and d.simulans , respectively ; these were chosen because the sibling species pairs can form fertile f1 hybrids and have been used to study genetic variation that underlies speciation .
a group called  assembly , annotation and analysis ( aaa ) has been coordinating the community production and distribution of the relevant large datasets , the production of consensus annotation sets and the preparation of the initial reports of the results of these studies ( ) . by the end of 2006
, it is expected that the major datasets will have been produced , publications submitted and data contributed to flybase and genbank . for each species
these data will include several independent homology - based and ab initio gene prediction sets , consensus mrna and protein annotation sets , orthologies , gene family groupings , and syntenic relationships among the species , the latter extending the previously known large - scale syntenic conservations among the chromosome arms of the genus drosophila ( see figure 2 ) .
the following discussion describes the major ways to interrogate and browse these genomes and their relationships to one another .
the flybase blast tool serves as a convenient entry point to data for the insect species for which genomic sequence data are available , including the 12 drosophila species , mosquito ( anopheles and aedes ) , silkworm , honey bee and tribolium .
the tool provides an array of options in an intuitive format ( figure 3 ) .
an extremely useful feature of the blast output presentation are links that go directly to a gbrowse view of the genomic region that corresponds to the blast hit .
the flybase blast tool .  blast database selection options are shown in the  blast database availability key and include the whole - genome assemblies , annotated transposons , protein sequences or intergenic sequences , as well as genbank and uniprot datasets .
the species for which data are available are shown in a hierarchical tree ; clicking on any node in the tree selects all descendants of that node .
not all types of data are available for each of the featured species : an availability code ( colored letters ) is shown after each species listing .
advanced blast options ( out of view at bottom of page ) allow customization of blast parameters and output format ; an on / off toggle is provided for the  low complexity filter ; the 
feature on genome map link shown at the top of an aligned segment ; this allows immediate access to a gbrowse view of the genomic region that corresponds to the blast hit , with the aligned region indicated by a gray panel .
interactive views of the data generated by the genomic sequencing projects are presented using a newly modified version of the gbrowse genome viewer [ ( 11 ) , ] .
entry to a specific genomic region may be accomplished by running a blast search first , as described above .
tools menu found in the top bar on all flybase reports . once the species to be viewed is chosen and the region of interest specified , the data to be viewed can also be specified and its presentation customized ( figure 4 ) . for the newly sequenced genomes
, the default view shows alignments to d.melanogaster putative orthologs and the gleanr consensus predictions .
gc content , translation stops and additional prediction sets may be selected for viewing , and the view may be modified by zooming or scrolling or flipping . as more data become available ,
datasets for the genomic extent being viewed may be downloaded as a decorated fasta file , a gff file or a table . a gbrowse view .
the region of the d.ananassae genome homologous to the d.melanogaster hp1c gene has been accessed via a link from the flybase blast output .
the default selection of data includes alignments of d.melanogaster putative orthologs and the gleanr consensus predictions ; in this view , additional gene prediction tracks have been selected .
the species being viewed may be changed at any time by choosing from the  data source menu .
once viewing the species of choice , a particular region can be specified using sequence coordinates or a 
landmark. for the newly sequenced species , the initial set of landmarks consists of the gene predictions , identified by their alphanumeric designations , and the d.melanogaster putative orthologs . the options for downloading the data shown are listed in the menu  reports and analysis ; the fasta output may be customized by using the 
data files for all classes of data in flybase are available for download by ftp in several formats , including gff3 for sequence data .
precomputed files option , at the top of all flybase pages ; from there , the  genomes : annotation and sequence section provides access to genome data for each ( or all ) of the sequenced species . in addition , bulk queries can be performed and downloaded via the 
from the  species menu on the top bar of the flybase home page and all report pages , additional information on the drosophilidae may be accessed . at present
there are four items to choose from :  phylogeny links to an index of species ,
synteny table goes to the presentation of syntenic relationships of the chromosomal arms of the 12 sequenced species shown in figure 2 ; 
drosophilidae links to a compilation of color images of species within this family , originally published by the university of texas at austin school of biological sciences ; and 
species resources will be updated periodically , as appropriate community resources and data become available .
now , availability and integration of genomic data for 12 well - characterized species provide a powerful resource that will allow the research community to take full advantage of the family drosophilidae as a model for comparative genomic and phylogenetic analyses .
 flybase ( ) is the primary database of genetic and genomic data for the insect family drosophilidae . 
 historically , drosophila melanogaster has been the most extensively studied species in this family , but recent determination of the genomic sequences of an additional 11 drosophila species opens up new avenues of research for other drosophila species . 
 this extensive sequence resource , encompassing species with well - defined phylogenetic relationships , provides a model system for comparative genomic analyses . 
 flybase has developed tools to facilitate access to and navigation through this invaluable new data collection . 
A NEW LOOK TO FlyBase
THE CHANGING CONTENT OF FlyBase
THE 
REPRESENTATION OF THE DOZEN GENOMES IN FlyBase
THE FlyBase BLAST TOOL: QUERIES ACROSS INSECT SPECIES
THE GBrowse GENOME VIEWER: CUSTOMIZED VIEWS OF PREDICTIONS AND EVIDENCE
BULK DATA DOWNLOADS
MORE ON THE SPECIES OF FAMILY DROSOPHILIDAE