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PileUp - how to align sequences > 7 kB

Lynn Miller miller at gcg.com
Tue Jun 23 11:17:08 EST 1998


Thomas Burmeister wrote:

> Dear Newsgroup-readers & GCG-users!
> I want to align sequences, appr. 10-15 kB in length. As I understand it,
> the GCG program PILEUP only supports alignments of sequences <= 7 kB. Is
> there a possibility to  circumvent this restriction? 

Though undocumented, there are three additional
versions of PileUp shipped with the GCG package that 
can be accessed and run just like the original:

Command:        Limits:
------------    -----------------------------------------------
pileup           5000 residues, 2000 gaps   =   7000 total
pileup_10000    10000 residues, 4000 gaps   =  14000 total
pileup_15000    15000 residues, 6000 gaps   =  21000 total
pileup_20000    20000 residues, 8000 gaps   =  28000 total

The versions with higher limits do require more memory to
run, and so I do not recommend making them the default versions.

Regards,
Lynn Miller, Technical Support Coordinator
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