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