SIMPLE34 - Detection of simple sequences

John Hancock John.Hancock at anu.edu.au
Thu Jan 6 21:57:36 EST 1994


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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.



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