FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.
Bottom Line: Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster, was released by the Berkeley Drosophila Genome Project in 2014; it replaces their previous Release 5 genome assembly, which had been the reference genome assembly for over 7 years.With the enormous amount of information now attached to the D. melanogaster genome in public repositories and individual laboratories, the replacement of the previous assembly by the new one is a major event requiring careful migration of annotations and genome-anchored data to the new, improved assembly.In this report, we describe the attributes of the new Release 6 reference genome assembly, the migration of FlyBase genome annotations to this new assembly, how genome features on this new assembly can be viewed in FlyBase (http://flybase.org) and how users can convert coordinates for their own data to the corresponding Release 6 coordinates.
Affiliation: The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA email@example.com.Show MeSH
Mentions: For the past decade, FlyBase has used the generic genome browser, GBrowse (16), for the display of genome annotations and genome-aligned evidence on the reference genome assembly. GBrowse allows users to navigate to a region of interest using coordinates or a landmark (e.g. a gene name or feature identifier), and from that entry point, zoom or scroll along the genome. The feature types displayed are user-selected. Genomic sequence for the region in view can be downloaded in a variety of formats. Concurrent with the introduction of Release 6, FlyBase has also upgraded to GBrowse 2 (23). GBrowse 2 retains the same functionality described above for GBrowse. However, GBrowse 2 contains some important upgrades, particularly its ability to handle much more data, which has allowed FlyBase to offer all D. melanogaster data options on a single view. GBrowse 2 also offers users easier track customization (vertical placement, open or hidden views) and limited smooth-track panning (side-to-side sliding). A new lasso feature can be used to select a region of interest, and either navigate to that region or download the associated genomic sequence (Figure 2). GBrowse 2 is accessible from the homepage and various FlyBase report pages.
Affiliation: The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA firstname.lastname@example.org.