Dave,
I was surprised to read your report. I recently aligned 12
Streptococcus pyogenes genomes (~1.8 Mb each) using the previous
release of Mauve on a G3 Mac. It took the program a few hours, but
it worked fine. I know that P. syringe has a larger genome than group
A streptococci, but I would have guessed that it would have aligned
them. Maybe there is also a memory issue? If not, what is the
theoretical genome size breakpoint for a 32 bit processor?
-Mike
On Jan 30, 2007, at 7:45 PM, David J. Schneider wrote:
Aaron,
I am interested in being able to perform a simultaneous alignment
of all of
the fully sequenced Pseudomonas spp. Attempts with previous
versions of
Mauve have been unsuccessful, apparently due to the 32 bit
addressing limit.
However, I have access to a Mac G5-based cluster with 8 Gbytes/
node. How
difficult would it be to produce a 64 bit version of Mauve for the G5?
By the way, the recently released progressive version works great and
appears to be significantly faster when aligning the three fully
sequenced
pathovars of P. syringae. The new search features are extremely
helpful.
Dave Schneider
Computational biologist
Pseudomonas syringae systems biology group
USDA Agricultural Research Service
W. Michael McShan, Ph.D.
Assistant Professor
Dept. of Pharmaceutical Sciences
P. O. Box 26901
CPB 307
University of Oklahoma Health Sciences Center
Oklahoma City, OK 73190
405-271-6593 ext. 47256
405-271-7505 FAX
405-517-2330 cellular
[EMAIL PROTECTED]
Knowing ignorance is strength.
Ignoring knowledge is sickness.
~Tao Te Ching
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