I presume you are talking about the PILEUP routine in the GCG package.
If you are, YES !!! there is a way to align sequences greater than 5 kb.
We modified the PILEUP routine (as per instructions in the GCG Users/
Administrators Guide) to create "BIGPILEUP", that allows us to align sequences
up to 15 kb. If I remember right, the limitation is 32-35 kb sequence
alignments. Check your Users manual pages 7-9 to 7-10, the section on
"Memory Requirement" to change the virtual memory allocation of your
system. You'll also need to work with your system administrator on this since
it means changing system parameters.
Current "adjustable parameters" in the system ("GCG") file
MAXSEQNUM = 300 maximum number of sequences
MAXSURFACE = 2,250,000 maximum surface of comparison
MAXSEG = 5,000 maximum length of segment to be aligned
PADDING = 2,000 maximum length of all gaps combined
What you want to change is MAXSEG. The GCG manual says, " The
'Changing Virtual Memory Requirements' chapter in the *Installation* section
of the *System Support Manual* contains instructions for your system
manager on how to modify, recompile, and relink PileUp".
Hope this helps. Regards, Chris.
Christopher M. Smith
School of Biological Sciences
University of Nebraska
Lincoln, Nebraska 68588-0118
csmith at crcvms.unl.edu