On 11 Jul 2003, Tim Cutts wrote:
> In article <e818c15b.0307100440.58d9f00b at posting.google.com>,
> Marcus Claesson <m.claesson at student.ucc.ie> wrote:
> For bacterial genomes, BLAST is probably fast enough. For mammalian
> genomes it isn't (unless you have many hundreds of CPUs available, which
> only a few sites do).
How about using MUMmer to localize the regions of the sequnce where
quality improvements (i.e. changes in the sequence) occured. MUMmer is
really fast even when comparing whole genome sequences.
After that you could run the ORF finding and blast the new agains the old
protein sequences. This would kill the "duplicate gene" problem.
Tim, you´re right. When talking about very small changes like indels, it´s
really hard to find the differences.