<From: DIN::"BIOSCI-REQUEST at net.bio.net" 20-SEP-1994 10:31:23.36
<To: info-gcg at net.bio.net
<CC:
<Subj: GCG version 8.0
<I just received in the mail an order form for buying the User's Guide and
<Program Manual of GCG Wisconsin Sequence Analysis Package version 8.0.
<We have the manual for version 7.x. Could someone from GCG post a list of
<the new features of version 8.0 so I can convince my boss that it is worth
<spending money on the new manual?
<Thanks in advance.
<Can Bruce
<Division of Molecular Medicine, Columbia University, New York.
Here is the listing you requested. At the end is a section on documentation
changes.
Maggie Smith
GCG
smith at gcg.com
NEW PROGRAMS SUMMARY
Prime
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.
NoOverlap
NoOverlap identifies the places where a group of nucleotide sequences
do not share any common subsequences.
BLAST
BLAST searches a specified database to find sequences that are similar
to a query sequence. BLAST either can search databases on your own
computer or it can search the databases maintained at the National
Center for Biotechnology Information (NCBI) in Bethesda, Maryland, USA.
ToBLAST
ToBLAST combines any set of GCG sequences into a database that you can
search with BLAST.
Distances
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.
This is a completely new version of the program. Distances was moved
from the Multiple Sequences Analysis chapter of the Program Manual to
the new Evolutionary Analysis chapter.
GrowTree
GrowTree creates a phylogenetic tree from a distance matrix created by
Distances using either the UPGMA or neighbor-joining method. You can
create a text or graphics output file.
FromFastA
FromFastA reformats one or more sequences from FastA format into
individual files in GCG format.
WPI: The New Graphical User Interface
GCG is introducing the Wisconsin Package Interface (WPI), a graphical user
interface based on OSF/Motif(TM). WPI runs on all systems that the Wisconsin
Package supports. To use the interface, you need an X Windows display, such as
an X terminal, an X server running on a PC or Macintosh, or a workstation that
runs X Windows.
WPI's main window is a list of sequences that interest you. You select one or
more sequences from the list in this window for analysis or display. Pull-down
menus allow you to manipulate sequences in the main window and show you the
sequence analysis programs available in the the Wisconsin Package. When you
select a program, a separate window specific for that program appears. The
program window displays the sequence or sequences you selected from the Main
List Window together with all of the parameters and options available for that
program.
When you click a program's RUN button, the output appears in a window called the
Output Manager. Clicking on any record in the Output Manager displays the text
or graphic you have chosen.
You can click on single sequences in the Main List Window to display them. This
display shows the text heading of the sequence as well as the sequence itself.
You can click and drag over any area of a sequence to specify a fragment upon
which you would like to do further analysis.
DOCUMENTATION CHANGES
PROGRAM MANUAL
A new section called Evolutionary Analysis has been added.
USER'S GUIDE
GCG has completely revised the USER'S GUIDE for Version 8. The new USER'S
GUIDE is designed for beginning users of the Wisconsin Package as
well as for intermediate to advanced users. It contains all of the
information in the previous version in addition to more detail. It
has been reorganized and now includes an index.
WPI GUIDE
The Wisconsin Package Interface WPI GUIDE is brand new to the GCG
documentation set. This comprehensive guide teaches you how to use the
Wisconsin Package via the new interface.
DATA REFERENCE SET
GCG has discontinued the DATA REFERENCE SET, Volumes 1 and 2, which
contained one-line descriptions of every database entry in GenBank, EMBL,
PIR-Nucleic, PIR-Protein, and SWISS-PROT.
We will continue to update and distribute the DATA FILES manual.
