FlyBase:Coordinate Converter

Coordinate Converter

The Coordinate Converter allows you to convert genomic coordinates between different genome releases. Just select the species, the input and output assemblies, enter your list of coordinates (or load them from a file), and away you go! It's that simple. The output page or file will list the input coordinates (with the release), the output coordinates (with the release), and notes on the conversion (e.g., "includes 1 area of change; different scaffold").

NOTE - this tool only converts from older to newer assemblies. A link at the bottom right is offered for reverse R6 -> R5 coordinates conversion.

NOTE - a link is provided for a standalone R5 -> R6 ID convertor script.

Species	Choose between D. melanogaster or D. pseudoobscura.
Send results to	Choose to send output to browser or downloadable file.
Input Assembly	Choose the assembly for the input coordinates. For D. melanogaster, options are Releases 3, 4 and 5.
Output Assembly	Choose the coordinates for the output coordinates. For D. melanogaster, options are Releases 4, 5 and 6 (current). NOTE - the output assembly should be a later version than the input assembly, otherwise there is an error. A link for a backwards R6 -> R5 converter is offered (see above).
Enter Drosophila Coordinates	Enter the coordinates to be converted, including the chromosome scaffold and either a single base position (e.g., 2RHet:1000) or a range (e.g., 2RHet:1-1000 or 2RHet:1..1,000). Chromosome must be separated from base position(s) by a colon, and when defining a range, used either a hyphen or two periods to separate the start and end sites. Numbers with or without commas are acceptable. Multiple coordinates, each on a new line, may be pasted into the box (up to a thousand or so).
Upload File of Coordinates	Alternatively, upload a file with the input coordinates, choosing the "Browse" button to search for the file.