how do I automatically update gene coordinates after re-sequencing the genome

Tim Cutts timc at chiark.greenend.org.uk
Mon Jul 14 13:45:32 EST 2003


In article <beu65u$8q5s2$1 at ID-144096.news.uni-berlin.de>,
Philipp Pagel <philipp.pagel at gmx.de> 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 many times per day did you upgrade your sequence? While it is
>definitely a good idea to throw a few CPUs at such a job I don't see why
>you would need hundeds of them. A BLAST search of all predicted mouse
>genes against a database of about the same size runs for only a few days
>on something like 10 CPUs.

Depends on how much else you have to do on the same machines.  :-)
You're probably right with modern machines.  At the time I was doing
this, I was running the analysis on a 250 MHz Sun E3000, and a handful
of Pentium II and Pentium III PCs...  At the time, we did have to do
this quite frequently, since we were building genes on the (then
frequently changing) HTG contigs.

Even so, the point is that there are much faster (and probably more
appropriate) tools for doing this than BLAST, especially for small
features.

Tim

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