In response to the nameless newsposter's question:
> Are there any changes in version 8.0 (I assume this is the latest) that make
> significant improvements for the end user?
I guess it depends on what you mean by "end user", and what s/he
would consider to be a "significant improvement".
FYI, GCG V8.0 includes several useful new programs:
o Prime, about which GCG says, "Prime selects oligonucleotide
primers for a template DNA sequence. The primers may be useful for
the polymerase chain reaction (PCR) or for DNA sequencing. You can
allow Prime to choose primers from the whole template or limit the
choices to a particular set of primers listed in a file."
o Blast, GCG's version of the Blast program, which can be used
in network client mode with the Blast server at NCBI (although that
service will cease some day)
o Completely new version of Distances program, about which GCG
says, "Distances creates a table of the pairwise distances within a
group of aligned sequences. A number of distance correction methods
are provided, including Jukes-Cantor, Kimura two-parameter, and Jin-
Nei gamma distance methods. The distance matrices produced by
Distances are suitable for input into the new GrowTree program for
constructing and displaying phylogenetic trees."
o GrowTree, which "creates a phylogenetic tree from a distance
matrix created by Distances using either the UPGMA or neighbor-
joining method."
o NoOverlap, which "identifies the places where a group of
nucleotide sequences do not share any common subsequences."
I consider these to represent a significant improvement. Our users
who run Prime a lot certainly consider *it* to provide significant
functionality which didn't exist in the GCG package before.
For users with X windows display capability, V8.0 also contains the
WPI (Wisconsin Package Interface), GCG's first formal offering of a
GUI (i.e., menus-and-windows interface) for the package.
Independent of the WPI's own style, which you may or may not like,
the interaction embedded in it has at least one definite improvement
over the GCGs of times past.... In WPI, commonly used analysis &
display program pairs:
Compare - DotPlot
WordSearch - Segments
MapSort - PlasmidMap
MFold - PlotFold
PeptideStructure - PlotStructure
StemLoop - DotPlot
have their executions linked by default. For example, if you
initiate a Compare operation, upon its conclusion the WPI auto-
matically runs DotPlot, displaying the output in a new X window.
That's one less step for the user to have to take.
Those are the significant augmentations which I have noted.
Mark Reboul
Columbia-Presbyterian Cancer Center Computing Facility
mark at cuccfa.ccc.columbia.edu
