Do you mean that you want to convert the coordinates of features based on an older version of a genome to those of a newer version of the same genome? (Or the reverse?). And possibly extract fasta genome sequence for those features?
If so, the tool LifeOver can be used. It is available in Galaxy in the tool panel. Not all genomes are supported but most are or can be added if they are sourced from UCSC.
This tool is based on the Batch Coordinate Conversion utility from UCSC and is also available for use at their website.
If your genome-to-genome mapping is not available in Galaxy yet, but the chain/liftover files from the Conservation track at UCSC exists, let me know and we can help with the request.
Thanks! Jen, Galaxy team