chas@stork.bcm.tmc.edu (02/17/88)
From: Charles Lawrence <chas@stork.bcm.tmc.edu>
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Gene and Protein Sequence Analysis for Sun Workstations
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The Molecular Biology Information Resource (MBIR) distributes a
software package for gene and protein sequence analysis that runs on
Sun workstations. EuGene, a newly developed easy-to-use interface,
creates a total environment for the execution of programs. The package
is a comprehensive set of standard software tools with graphics
capabilities. Sequence alignment programs implementing the Feng and
Doolittle multiple alignment algorithm and phylogenetic tree analysis,
a modified Needleman-Wunsch alignment program, and a program that
searches for homology domains are among several of the homology
programs available. Also included are a suite of programs which
predict secondary structure and hydropathicity patterns of peptides.
The design of the interface makes it useful both for individuals with
limited computer experience, as well as for those with advanced
application needs.
EuGene is a menu-driven system, complete with concise on-screen advice
and extensive on-line help. An "object inventory" organizes the user's
sequences and data objects. A user can maintain different "projects",
each having separate object inventories with options for moving data
from project to project. Built-in editors are used to enter sequences,
to modify the text output produced by the software tools, and to keep
notes in an electronic notepad. The interface can be used from
standard terminals or PCs emulating a standard terminal. Graphic
output is in Tektronix 4014 format and can be sent automatically to a
"Tek4014" window when using a Sun, or displayed on a PC using a
terminal emulator that supports Tektronix 4014.
For more information about EuGene, contact:
Sandra Honda, Ph.D.
Molecular Biology Information Resource
Dept. of Cell Biology
Baylor College of Medicine
One Baylor Plaza
Houston, TX 77030
713-799-4275
E-mail: eugene@mbir.bcm.tmc.edu
sandra@mbir.bcm.tmc.edu
******************************************************************************elliston@rob.UUCP ( Keith Elliston) (06/22/89)
Hello: I am doing some sequence analysis on proteins, and need a program to determine the amphipathic helicity of specific proteins. I have modified the program of Margalit et al (J. Immunology 138:2213-2229, 1987) to work within the GCG sequence analysis package. But, I would like to be able to use different hydrophobicity scales, other than the Fauchere-pliska scale. My question is this... which scales would be compatable, and what is a good reference for them? Also... are there any other programs for doing this kind of analysis? Additionally, I need a program to design oligonucleotides, based upon a peptide sequence. What I need the program to do is to look at a known peptide sequence and determine the best site for reverse engineering an oligo probe. it should look for the best Tm range, and the fewest possible permutations of the sequence (e.g., find Met and Phe codons and etc....). Anyone have such a program, or know where I can find one. If someone has fortran code for it, I can modify it to run on my system (did I mention that I am running a Vax 8820 under VMS, so anything that runs here is most appreciated). One more thing... is there a group that is dedicated to sequence analysis, and the tools for doing same? If not, I think that such a group would be of wide interest, and considering that most of us who do seq. anal. extensively are rather computer literate, I think such a group would see extensive use. Thanks for the info.... Keith =============================================================================== Keith O. Elliston | Usenet: uunet!rob!elliston Senior Information Scientist | Arpanet: rob!elliston@uunet.uu.net Merck Sharp & Dohme Res. Lab. | Bitnet: elliston%rob.uucp@psuvax1 Rahway, NJ 07065 U.S.A. | -or- elliston@biovax =============================================================================== Disclaimer: I can have no OFFICIAL comments about anything........ ===============================================================================
kristoff@NET.BIO.NET (David Kristofferson) (06/28/89)
Keith, The BIO-SOFTWARE group is the appropriate place for people interested in sequence analysis to hold their discussions since this bulletin board grew out of organizations such as SEQNET and BIONET which are primarily interested in this problem. Although BIO-SOFTWARE also covers a broader range of topics, it makes sense not to split off a separate newsgroup until the volume warrants it. -- Sincerely, Dave Kristofferson BIONET Resource Manager kristoff@net.bio.net or kristofferson@bionet-20.bio.net