Download Sequence Analysis Guide 2

originally developed by the Genetics Computer Group,
Inc. (GCG, Inc.); a spinoff company of the University of
Wisconsin. The Wisconsin Package is currently a part of
Accelrys Corp (http://www.accelrys.com/). The Vector
NTI package was developed by the InforMax Inc., and
now is a product of Invitrogen Corporation
(http://www.invitrogen.com/).
Besides the above commercial software, several freeware
packages are installed on computers at both facilities.
These include PHYLIP, a well-known program for
phylogenetic analysis, and ClustalW, a reputed program
for sequence alignment. In addition, there are web-based
programs (e.g., EMBOSS, SRS,
Entrez, ReadSeq,
Primer3)
available
at
the
BCRF
website
(http://biocore.unl.edu), allowing the user to run them
though a web browser.
The Wisconsin Package
The Wisconsin Package follows a toolbox philosophy in
software design, meaning that the package consists of
many small programs (tools) as opposed to one large and
complex integrated application. The Wisconsin Package
was developed as a text-mode, command-line driven set
of programs: the user interfaces with the computer by
typing text commands. As windowing, mouse "clickable"
menu systems became popular with the availability of
more powerful inexpensive computers, GCG developed
an X Windows based version of the Wisconsin Package.
That graphical user interface to the Wisconsin Package,
known as SeqLab is available on gsaf and biocomp2.
SeqLab users can also learn the commands to use the textmode prompt in order to use the programs via a modem or
from systems which do not support an X Windows server.
Note that some of the command line GCG programs
produce graphical output. Methods to view these plots
without running SeqLab or to have them saved as
postscript files for printing will be shown in Chapter 2.
The Wisconsin Package (or GCG package) consists of
several sequence databases and a variety of powerful
sequence analysis tools. It is available for use on
computers running UNIX or Linux operating systems.
The computational power offered by the workstation
environment frequently provides the Wisconsin Package
programs a significant performance advantage over
comparable personal computer-based software. In
particular, sequence alignments and phylogenetic tree
constructions will take a few minutes or hours instead of
days on a PC. Software and database updates handled by
the system administrator(s), along with access to remote
databases, guarantee the user access to the most up-todate information and analysis tools available.
There is also a web interface to GCG called SeqWeb. To
utilize this, you must have a SeqWeb account. For
security reasons, your SeqWeb account is different from
your regular account on gsaf or biocomp2. These are
available by application through the web at
http://molbio.unmc.edu/
(UNMC
members)
or
http://biocore.unl.edu (UNL members). The Web browser
interface requires specific versions of Netscape or Internet
Explorer for PC or Macintosh users. See Chapter 3 for
more details.
3
4
Vector NTI
The Vector NTI package runs on a Windows or
Macintosh computer. Most biologists are familiar with