FlyBase: genes and gene models

Abstract

FlyBase (http://flybase.org) is the primary repository of genetic and molecular data of the insect family Drosophilidae. For the most extensively studied species, Drosophila melanogaster, a wide range of data are presented in integrated formats. Data types include mutant phenotypes, molecular characterization of mutant alleles and aberrations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions. There is a growing body of data for other Drosophila species; this is expected to increase dramatically over the next year, with the completion of draft-quality genomic sequences of an additional 11 Drosophila species.

Figure 1

FlyBase gene report, highlighting different format and subsection report options, automated gene summaries and the recently added External Database section.

Figure 2

FlyBase annotation report. The panels show sequential extracts from the annotation report. At the top there are links to a Cytogenetic map, the GenBank scaffold sequence accession, and a Peptides ‘view analysis’ page showing alignments to related proteins and protein domain predictions. The ‘Sequence’ option allows the user to retrieve sequence for the gene region, transcripts, UTRs or proteins in a choice of formats. The Gene Annotation and Evidence panel shows two alternative transcripts and supporting EST, cDNA and protein (blastx) data. Note that the mle-RB transcript is based on data curated from the literature (not represented graphically), and that cDNA data supports an additional alternative transcript (to be added in the next annotation update). Details about the annotated transcripts and protein products are presented, and an ‘Other Features’ section describes mutational lesions, rescue fragments and other entities mapped onto the sequence level. These features appear on the GBrowse map, which may be accessed from a link at the top of the page.

Figure 3

The FlyBase ‘Batch Download Reports by ID’ tool. In this example, seven genes are the subject of the query (listed in the ‘Enter List of Ids’ box), the user has selected ‘Document hypertext’ as the output format, and is in the process of selecting which data fields to retrieve.