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Version 1.0 of SIMPLE34 is available free of charge to
academic users.
-> WHAT DOES IT DO?
SIMPLE34 extends and makes more widely available the SIMPLE
program originally described by Tautz, Trick & Dover
(Nature 322, 652-656, 1986). Details of this implementation
will be published in 1994 in CABIOS.
The aim of the program is to estimate the level of local
sequence repetition in nucleotide sequences. It does this
by analysing the degree of clustering of short sequence
motifs (3- and 4-mers). A significant level of clustering
of short motifs has been suggested to reflect the action of
replication slippage in the recent evolutionary history of
sequences and is associated with length polymorphism in a
variety of sequences including ribosomal RNAs, the
mitochondrial control region and the transcription factor
TBP.
The program provides the following information:
-- A measure, the RELATIVE SIMPLICITY FACTOR (RSF), which
represents the degree of motif clustering within the
sequence relative to random sequences of the same base
composition, doublet composition and length as the input
sequence. The program calculates confidence limits for the
level of motif clustering within the sequence being
statistically significant.
-- A graphical representation (in POSTSCRIPT format) of the
distribution of motif clustering along the sequence.
-- The locations of sites showing significantly more motif
clustering than is seen in the random sequences.
-- The sequence motifs associated with significantly high
levels of clustering.
A detailed description of the operation of SIMPLE34 can be
found in the file simple34.doc included with the program.
-> PLATFORMS
SIMPLE34 is written in FORTRAN77 and is available for Vax
and Sun platforms.
-> AVAILABILITY
SIMPLE34 can be obtained over the network from the
Australian National University by anonymous FTP or Gopher.
Anonymous FTP:
Host Name: life.anu.edu.au
Directory: /pub/molecular_biology/software/simple
Subdirectories software/vax and software/sun
contain the directories simple34. FTP the
complete directory for best results.
File types: Text
Gopher:
Name = simple34
Host = life.anu.edu.au
Path = /molecular_biology/software/simple
Subdirectories software/vax and software/sun
contain the directories simple34. FTP the
complete directory for best results.
-> HOW DO I USE SIMPLE34?
SIMPLE34 accepts plain (Staden) format RNA or DNA sequences
up to 50,000 bases in length.
Instructions for setting up the programs are included in
the readme files accompanying the two versions. Running the
script/command procedure "setup" will compile the program.
For Vax users, instructions for adding aliases for the
command procedures that come with the program are included
in the readme file. This is done automatically on Sun
systems.
-> WHO CAN I CONTACT ABOUT SIMPLE34?
Comments, suggestions for improvements and gripes can be
sent to John Hancock at the following addresses:
E-mail: John.Hancock at anu.edu.au
Phone: +61-6-249-5916
Fax: +61-6-249-4437
Post: Research School of Biological Sciences,
Australian National University,
Canberra,
ACT 0200,
Australia.
