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. 2015 Jan;43(Database issue):D690-7.
doi: 10.1093/nar/gku1099. Epub 2014 Nov 14.

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

Gilberto dos Santos  1 , Andrew J Schroeder  2 , Joshua L Goodman  3 , Victor B Strelets  3 , Madeline A Crosby  2 , Jim Thurmond  3 , David B Emmert  2 , William M Gelbart  2 ; FlyBase Consortium
Affiliations

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

Gilberto dos Santos et al. Nucleic Acids Res. 2015 Jan.

Abstract

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.

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Figures

Figure 1.
Figure 1.
Coordinates Converter. This tool can be accessed by the ‘Tools’ menu in the blue navigation bar found at the top of FlyBase pages, under both the ‘Retrieve/Convert’ sub-menu (shown) and the ‘Genomic/Map Tools’ sub-menu. A variety of input formats are accepted, and input lists may be uploaded from a text file or entered directly into the input box; output may be to a browser view or a downloadable file (menu at upper right). By default, the input assembly is set to Release 5 and the output to Release 6, but other forward conversions can be specified. For conversion from Release 6 back to Release 5, an analogous Coordinates Converter tool is provided (link at lower left).
Figure 2.
Figure 2.
GBrowse 2. Like the original GBrowse, GBrowse 2 allows users to navigate to a region of the genome using coordinates or a landmark, and zoom or scroll along the genome to browse annotated features and aligned evidence; the data tracks shown are user-selected; genomic sequence for the region in view can be downloaded by selecting ‘Download Sequence File’ in the download option menu at the top right. However, GBrowse 2 can handle more data and has convenient new features. Tracks can be moved simply by dragging the track title bar vertically, and hidden or removed by clicking on the appropriate boxes within the track title bar. In GBrowse 2, one can also download sequence for a smaller region within view by lassoing the region (as shown for a 1.4-kb region within the 6-kb view) and selecting ‘Dump selection as FASTA’ from the resulting pop-up menu (far right).
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