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

dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM, FlyBase Consorti - Nucleic Acids Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA dossantos@morgan.harvard.edu.

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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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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).

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.


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

dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM, FlyBase Consorti - Nucleic Acids Res. (2014)

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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
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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).
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.

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.

View Article: PubMed Central - PubMed

Affiliation: The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA dossantos@morgan.harvard.edu.

Show MeSH