how do I automatically update gene coordinates after re-sequencing

[Marcus Claesson]

Thanks, that's looks promising! I'll have a look at that. 
However, after I sent out my question I found a public
program that seem to solve the problem at least for prokaryotes. It's
Sequin at http://www.ncbi.nlm.nih.gov/Sequin/

It has quite a nice feature that checks the differences between old
and new sequence, let you scroll thorugh them and then updates. The
input is fasta format and a tab-separated textfile with annotations.
Sequin then creates a genbank entry that can be updated with new
sequence in fasta format.

My problems now seem to be solved :))

Mrcus

> 
> Use the NUCmer wrapper for the MUMmer whole-genome alignment program,
> 
>    <http://www.tigr.org/software/mummer/>. 
> 
> A brief discussion of NUCmer may be found in the MUMmer manual,
> 
>    <http://www.tigr.org/software/mummer/manual/#alignment>,