I am an user of GCG package, more precisely of multiple sequence analysis
(MSA). But there, I don't really see any means to see significance of scores
generated by profilesearches i.e. score distribution plots which truely are
the graphic representation of the performance of probe sequences against an
average database. The size of databases has doubled and I find many interesting
sequences but even after GCG release 6.2, still, I manipulate all the data
manually to construct histograms, where neither the time is saved nor a good
quality is achieved. Recently in "Methods of Enzymol."(vol. 183) in an artical
on Profile analysis by Gribskov et al., the Z-score distribution plots of even
better representation have been shown.
Any advice or means on this recurring problem are gratefully acknowledged.
der Universitaet Zuerich
E-mail: jaimatadi at sys.ife.ethz.ch