Lift Genome Annotations

This tool converts genome coordinates and genome annotation files between assemblies.  The input data can be pasted into the text box, or uploaded from a file.  If a pair of assemblies cannot be selected from the pull-down menus, a direct lift between them is unavailable.  However, a sequential lift may be possible.  Example: lift from Mouse, May 2004, to Mouse, Feb. 2006, and then from Mouse, Feb. 2006 to Mouse, July 2007 to achieve a lift from mm5 to mm9.  

Original Genome: Original Assembly: New Genome: New Assembly:


Minimum ratio of bases that must remap:
BED 4 to BED 6 Options
Allow multiple output regions:
  Minimum hit size in query:
  Minimum chain size in target:
BED 12 Options
Min ratio of alignment blocks or exons that must map:
If thickStart/thickEnd is not mapped, use the closest mapped base:

 Paste in data (BED or chrN:start-end formats):

 Or upload data from a file (BED or chrN:start-end in plain text format):

Command Line Tool

To lift genome annotations locally on Linux systems, download the liftOver executable and the appropriate chain file. Run liftOver with no arguments to see the usage message.