GCG version 8.0

Maggie smith at GCG.COM
Tue Sep 20 16:35:17 EST 1994

<From:	DIN::"BIOSCI-REQUEST at net.bio.net" 20-SEP-1994 10:31:23.36
<To:	info-gcg at net.bio.net
<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 

Maggie Smith
smith at gcg.com

                         NEW PROGRAMS SUMMARY


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 identifies the places where a group of nucleotide sequences
do not share any common subsequences.


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 combines any set of GCG sequences into a database that you can
search with BLAST.


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 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 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

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


A new section called Evolutionary Analysis has been added.


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. 


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. 


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.

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