FlyBase: integration and improvements to query tools

Abstract

FlyBase (http://flybase.org) is the primary resource for molecular and genetic information on the Drosophilidae. The database serves researchers of diverse backgrounds and interests, and offers several different query tools to provide efficient access to the data available and facilitate the discovery of significant relationships within the database. Recently, FlyBase has developed Interactions Browser and enhanced GBrowse, which are graphical query tools, and made improvements to the search tools QuickSearch and QueryBuilder. Furthermore, these search tools have been integrated with Batch Download and new analysis tools through a more flexible search results list, providing powerful ways of exploring the data in FlyBase.

Figure 1.

QueryBuilder results. The results of a two step QueryBuilder search to identify GAL4 insertions expressed in the wing or which are associated with wing phenotypes are shown. Each query leg appears at the top of the page. The columns in a hit list are dependent on the data class being searched. Each column can be sorted by clicking the small arrows on either side of the column header. Records are selected for further manipulation via the checkboxes at the left; all hits are selected by default.

Figure 2.

Results Analysis/Refinement Tool. The Results Analysis/Refinement Tool has been used to display the distribution of Biological Process controlled vocabulary terms applied to a list of the components of the Notch signaling pathway. The second column displays the term for which the distribution was created. The next three columns show a graphical display, the raw size, and the relative size of the term in the distribution. Clicking on the number in the ‘Related records’ column will return a hit list containing the individual records that make up that bin.

Figure 3.

Interactions Browser. The options at the top of the page of the Interactions Browser permit the selection of different types of interaction data and adjustment of the scan depth, which refers to the number of interaction steps shown from the query. The ‘auto’ value set for the scan depth by default chooses a number based on the complexity of the data. In the diagram, the alleles or genes that interact directly with the query allele or gene are shown in dark blue, and alleles or genes that interact with them are shown in light blue if the scan depth is set to 2. The program uses different colored lines to indicate the type of interaction and arrows to denote the direction in which the interaction was recorded. In some interaction diagrams that have many alleles or genes, the symbols can overlap making it hard to identify them. To view this data the picture can be redrawn in another orientation by choosing a different rotation factor.

Figure 4.

GBrowse. The ‘OrthoView’ of GBrowse shows an alignment of one of the newly sequenced Drosophila genomes with the genome of D. melanogaster. The alignment of putative orthologs within the region displayed is indicated by green lines connecting the two genome views. Information about the D. melanogaster genes displayed is provided in a pop-up window when you place your mouse over a gene span. Each gene and transcript within the D. melanogaster genome view is linked to a detailed report page and this function will be extended to the other genomes when report pages are created.