The Hartwell Center has provided the GCG software suite for analyzing
protein and nucleotide sequences for years, as well as the related programs
SeqLab and SeqWeb suites. However, these programs are no longer being
developed or supported by their vendor, Accelrys, as of September 30th. As
a result, GCG and its associated programs will not be available at St. Jude
after September 30th.
Data generated using GCG Command Line or SeqLab will still be available in
the current directories. Users will not be able to log into GCG Command
Line or SeqLab to access this data, but will need to access it via a network
drive.
We will maintain an archive of the data in the SeqWeb user directories. If
you require access to data generated using SeqWeb, it will need to be moved
to a different directory. We will execute this only at the user's request.
Please contact hartwell.systems@stjude.org for assistance with accessing
legacy data generated in GCG Command Line, SeqLab or SeqWeb.
The Hartwell Center provides and supports the Lasergene sequence analysis
software, with a 34 concurrent user network license and training sessions.
Please visit http://www.hartwellcenter.org/news/DNASTAR.php for more
information.
A free and widely used alternative to GCG will remain available, called
EMBOSS. Like GCG, EMBOSS consists of over a hundred command-line programs
for aligning sequences, scanning for restriction enzyme sites or other
motifs, creating consensus sequences, editing alignments, translating
nucleotide sequences, generating reverse complements, removing vector
sequences and repetitive elements, and many other common analysis tasks.
EMBOSS operates well with related free software like ClustalW, Phylip, and
Staden. Graphical interfaces and web interfaces to EMBOSS programs are also
freely available. More information about EMBOSS is available on their
website:
Users with accounts on the Hartwell Center's Linux cluster
(portal.web.stjude.org) can already use EMBOSS, and others should contact
Scott Malone (scott.malone@stjude.org) to get an account on the cluster.
EMBOSS can also be downloaded for desktop use on Linux or other Unix
computers at the EMBOSS link above, and versions for Mac OS X and Windows
have recently become available.
A web interface called EMBOSS Explorer will also be installed in the
Hartwell Center and provided to the St. Jude community in the near future.
For any needs not covered by LaserGene or EMBOSS, please contact the
Hartwell Center's Bioinformatics group (hartwell.bioinformatics@stjude.org)
for help.
