Download ramha1 - University of Toronto

I have just sent the IBM-PC program RAMHA to the following archives:
EMBL: embl-heidelberg.de
(uuencoded self-extracting LHARC file)
Indiana: ftp.bio.indiana.edu
(self-extracting LHARC file + readme
file)
Toronto: ftp.cs.toronto.edu
(Both:
uuencoded self-extracting file RAMHA1.UUE
& self-extracting LHARC file RAMHA1.EXE)
U.Houston: evolution.bchs.uh.edu (uuencoded self-extracting LHARC file)
RAMHA: Monte Carlo simulation of the random mutagenesis of synthetic
cDNAs
David P. Siderovski
Department of Medical Biophysics, University of Toronto,
Toronto, Ontario M4X 1K9 CANADA
INTERNET: [email protected]
RAMHA version 1.0 is provided as a self-extracting LHARC archive
(RAMHA1.EXE) containing the simulation program, all associated support
files,
and a user's manual. To extract the files, just type RAMHA1 at the DOS
prompt.
Random mutagenesis is a powerful tool in protein structure-function
analysis.
One approach is the synthesis of cDNA sequences using doped nucleoside
phosphoramidites. A Turbo PASCAL program, RAMHA, was written for
modelling this method of random cDNA mutagenesis on PC-compatible
computers.
Editing facilities allow the target cDNA to be entered directly as
nucleotide
sequence or by back-translation of the encoded polypeptide, as entered
using
one-letter amino acid abbreviations; back-translation is based on predefined
codon frequency tables supplied for several common research organisms or
on
user-defined tables as created within RAMHA. Sequences can also be
imported from and exported to GCG sequence file format.
After a target cDNA has been entered or imported into RAMHA, the user can
directly simulate the random mutagenesis of this sequence.
Several parameters controlling the mutagenesis simulation can
be specified, including nucleotide doping level, number of iterations of
the
simulation algorithm, and sequence(s) of enzyme site(s) to be detected
within
"synthesized" oligos. The user can also test a range of nucleotide
doping
levels using batch execution.
RAMHA will then simulate the synthesis of a user-specified number of
oligos, translate each into polypeptides, and accumulate various
statistics,
including average percent similarity of mutant proteins to wildtype
sequence,
frequency of resultant proteins retaining wildtype sequence, and percent
of
premature open-reading frame terminations. In addition, RAMHA can scan
"synthesized" genes for new internal restriction sites arising from
nucleotide
substitution and report on "hotspots" within the wildtype cDNA sequence.
By accumulating data on the number and position of stop codons (TAA, TAG,
TGA)
arising in "synthesized" oligonucleotides, RAMHA can report on the
frequency of premature open-reading frame terminations & the number of
mutant
proteins truncated before the end of a critical domain. Tests on a cDNA
containing all possible codons have revealed the requirement
for two distinct "anti-termination" strategies, schemes circumventing the
random introduction of stop codons (TAG, TGA, TAA), which have been added
to
the algorithm.