Unix software for hydrophobicity

Harry Mangalam mangalam at UCI.EDU
Thu Sep 30 12:31:43 EST 1993


>Unfortunately, the code appears to have been translated from Fortran to
>C using f2c, so to compile it I need libraries I don't have. Also,
>there are some references to arrays that aren't declared in the file,
>as if alom.c is part of a larger package. Anyway, I'm stumped.
>My question :  is there C code around that I can use to find putative
>transmembrane regions given a sequence of amino acids?
>
>Thank you for your attention to this matter,

Yo, Bob,

   You might try Russ Doolittle at UCSD (rdoolittle at ucsd.edu; (619)
534-4417).  At one point he had a program called "grease" that would do
this sort of thing - I believe that it's in C and is PD (don't bother with
archie - all it picks up are files related to the musical).  Alternatively,
if you are looking for specific types of transmembrane regions, you might
try the "profiles" approach of Gribskov and Eisenberg using the GCG suite
if that's available to you.  I'm sure that there are many other similar
programs freely available, though perhaps not the source code.
   Actually I believe that Kay Hoffman's Prograph suite (for the PC)
contains such a program. He (note HE) *may* be willing to make the code
available for academic purposes if it's not already.  The programs are
available from Don Gilbert's ftp archive (ftp.bio.indiana.edu) in the PC
directory.

   And no, I still haven't gotten NeXTSTEP up and running yet (haven't
managed to grab a 486 motherboard), but I've almost gotten Linux up on my
386.

Harry





More information about the Bio-soft mailing list