DNA* and Jotun Hein Alignments

Andy Law Andy.Law at bbsrc.ac.uk
Mon Jul 13 03:15:56 EST 1998

In article <19980712115818.419772d7.in at genvec.com>, "Lou Cantolupo"
<lou_cantolupo at genvec.com> wrote:

 >  Has anyone ever tried to do a Jotun Hein alignment on DNA* (for the Mac)
 >  and gotten it to work?!?!  It seems that I always run out of memory.  I'm
 >  not asking it to do anything real complex either.  I never got it to work
 >  on my old 68040 (which had 32megs of RAM).  Now I have a new 266 G3 with
 >  128Mb and I still can't get it to take four 300bp sequences and do an
 >  alignment without running out of memory!!!  And yes, I've gone to the 'Get
 >  Info' option and have allocated 90Mb of RAM and taken it off the network and
 >  it still only get's 50% though it before giving the "not enough memory"
 >  crash.

I can confidently state that I have never got DNAStar on the Mac to provide
me with a single alignment. I confess that I have not tinkered heavily with
the default parameter settings, naively assuming that two closely related
sequences would be pretty simple to align. There is only so much time that
you can spare for these things. We all tend to be on three year contracts
and I get the feeling from other's experiences that it mught take all of
those three years to get it to eork just once. We use our GCG/EGCG system
on unix for that sort of stuff.

Andy Law
( Andy.Law at bbsrc.ac.uk )
( Big Nose in Edinburgh )

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