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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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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).
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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).

Mentions: Many researchers will want to convert the Release 5-based coordinates for their own data into the corresponding Release 6 coordinates. For small sets of data, FlyBase provides the Coordinates Converter tool, which converts genomic coordinates based on a specific genome assembly release to those for a later release. For each set of coordinates converted, the tool also reports if there have been any changes to the genomic sequence in that region between the assembly releases. For example, for the input Release 5 coordinates ‘2LHet:16,945..17,066’, this tool returns the corresponding Release 6 coordinates ‘2L:23,158,471..23,158,593’, with the notes ‘includes 1 area of change; different scaffold.’ The Coordinates Converter may be accessed from the ‘Tools’ menu on the navigation bar, and offers a number of input and output options (Figure 1). A separate Release 6-to-Release 5 backwards converter is also provided (Figure 1).


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)

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

License
Show All Figures
getmorefigures.php?uid=PMC4383921&req=5

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).
Mentions: Many researchers will want to convert the Release 5-based coordinates for their own data into the corresponding Release 6 coordinates. For small sets of data, FlyBase provides the Coordinates Converter tool, which converts genomic coordinates based on a specific genome assembly release to those for a later release. For each set of coordinates converted, the tool also reports if there have been any changes to the genomic sequence in that region between the assembly releases. For example, for the input Release 5 coordinates ‘2LHet:16,945..17,066’, this tool returns the corresponding Release 6 coordinates ‘2L:23,158,471..23,158,593’, with the notes ‘includes 1 area of change; different scaffold.’ The Coordinates Converter may be accessed from the ‘Tools’ menu on the navigation bar, and offers a number of input and output options (Figure 1). A separate Release 6-to-Release 5 backwards converter is also provided (Figure 1).

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