gilbertd@silver.ucs.indiana.edu (Don Gilbert) (11/27/90)
Notes on the compiled versions of the MacPROT package for Macintoshes
(Peter Markiewicz, 1990)
MACPROT
MACProt consists of a set of programs for analyzing protein
sequences for secondary structure, chain flexibility, hydropathy,
helical wheels, and so on. Each program is supplied in a separate
archive file. A list of the programs is given below.
PLOT.A/HYD analyses the hydropathy (hydrophobicity/
hydrophilicity) according to four published hydropathy scales of any
sequence stored in AA.DATA file format. The plot can be printed or
saved to the clipboard for pasting it into a picture accepting program.
After the plot is completed the same sequence can be analysed using
different parameters and/or a different hydropathy scale.
PLOT.A/HYD5 analyses the hydropathy of a given sequence.
It calculates and plots the hydropathy for five increasing moving
averages (spans) simultaneously. The first span and the step for the
increase is chosen by the user. Saving and printing is done as in
PLOT.A/HYD.
PLOT.A/SUM provides three hydropathy plots for a single
sequence simultaneously using three different hydropathy scales.
Saving and printing is done as in PLOT.A/HYD.
PLOT.A/H3 calculates and plots the hydropathy of up to
three sequences simultaneously. It can be chosen among four
hydropathy scales. Saving and printing is done as in PLOT.A/HYD.
PLOT.A/TMH calculates and plots the hydropathy. In
addition each value for the chosen span is evaluated for its
coordinates in a 'hydrophobic moment' plot and the corresponding
assignment to the helix type shown. The assignment is also written to
a disk file in ASCII format. Saving and printing is done as in
PLOT.A/HYD.
PLOT.A/HEL draws a helical wheel of a user selected span
of amino acids, plots the hydropathy, and calculates the mean
hydropathy using two scales. Saving and printing is done as in
PLOT.A/HYD.
PLOT.A/DOT plots two sequences (the same or different
ones) against each other in a dot matrix. Two methods are used,
which either search for perfect matches (identities) or for similarities
according to five different score matrices based on (a) accepted point
mutations, (b) genetic and structural similarities, (c) conformational
state, and (d) observed substitutions. Saving and printing is done as
in PLOT.A/HYD.
PLOT.A/GOR calculates and plots the preference of each
residue for four conformations (helix, extended, coil, turn) along the
sequence. The sequence is written to a file in coded letters according
to the most likely preference. Saving and printing is done as in
PLOT.A/HYD.
PLOT.A/GGR similarly calculates and plots the preference
for three conformations (helix, extended, coil) along the sequence and
writes the evaluation to a disk file. Saving and printing is done as in
PLOT.A/HYD.
PLOT.A/STR searches for up to ten user selected stretches
of amino acids within a given sequence and plots the respective
positions found along the sequence. Saving and printing is done as in
PLOT.A/HYD.
PLOT.A/FOT suggests regions likely to be amphipathic.
Two disk files are created (1) to specify the residue starting an
amphipathic segment, and (2) to write the sequence in coded format.
Saving and printing is done as in PLOT.A/HYD.
PLOT.A/POW plots the power spectrum of a user selected
stretch. Saving and printing is done as in PLOT.A/HYD.
PLOT.A/KAS determines main chain flexibility and in turn
antigenic determinants.
PLOT.A/TSL translates a DNA sequence.
Available from:
EMBL: NETSERV@EMBL GET MAC_SOFTWARE:filename.ext
U Houston: genbank-server@bchs.uh.edu (INTERNET/ARPANET)
SEND MAC hqx-encoded-file-name
America Online: New service summer 1990, consult your manual for
details
IUBIO: anonymous ftp to: IuBio.Bio.Indiana.Edu
directory: [archive.molbio.mac] (cd [archive.molbio.mac])
files included in this MACPROT package are:
PLOTA-DOC.HQX;1 106 28-SEP-1990 22:50
PLOTA-GGR.HQX;1 258 16-OCT-1990 13:21
PLOTA-HEL.HQX;1 300 18-SEP-1990 20:23
PLOTA-POW.HQX;1 241 5-NOV-1990 16:15
PLOTA-SIG.HQX;1 213 5-NOV-1990 16:19
PLOTA.HQX;1 390 19-SEP-1990 14:31
PLOTA.README;1 32 17-AUG-1990 13:31
PLOTGOR.HQX;1 263 19-NOV-1990 17:16
PLOTKAS.HQX;1 209 4-OCT-1990 11:40
PLOTKKD.HQX;1 205 19-NOV-1990 17:17
PLOTTMH.HQX;1 223 19-NOV-1990 17:19
Written by:
Peter Markiewicz
Dept. Microbiology, MBI, UCLA
Los Angeles, CA 90024
email: JMILLER%VXBIO.SPAN@STAR.STANFORD.EDU
- - - - - - - - - -
Don.Gilbert@Iubio.Bio.Indiana.Edu
biocomputing office, indiana univ., bloomington, in 47405, usa