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 :))
>> Use the NUCmer wrapper for the MUMmer whole-genome alignment program,
>> A brief discussion of NUCmer may be found in the MUMmer manual,