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Announcement: New program for designing degenerate oligos

ramin homayouni ramin at brain.bchs.uh.edu
Wed Jan 12 18:05:39 EST 1994


I'm announcing a new program (called DegenDesigner 1.0) that can be used to  
design degenerate oligos (for PCR or blotting).  Currently, DD only runs on  
NeXT machines running Nextstep version 3.0 or above.  It is available for free  
by anonymous ftp from:
evolution.bchs.uh.edu in the /pub/gene-server/unix directory.

DD is different from any other available program in that it tests the selected  
degenerate oligos for inter- and intramolecular secondary structure formation  
at various temperatures.  In addition, DD contains an online help manual which  
includes a few fundamental references. 

Here is a copy of the the Readme file accompanying the program:
------------------------------------------------------------------------------- 
-DegenDesigner 1.0
Sept. 1993


GENERAL INFORMATION:
  DegenDesigner (DD) is a program which aids in the selection of degenerate  
oligonucleotide sequences from a given peptide sequence.  The program only runs  
on NeXTs running Nextstep 3.0.
DegenDesigner Will allow the user to:
  1. Backtranslate a peptide sequence to its corresponding nucleotide coding  
sequence.  
  2. View all potential forward and reverse primers (within a user-specified  
length range) that do not exceed a user-selected degeneracy limit (up to a  
maximum of 256 fold).  For each primer, DD will display the primer length,  
start position, degeneracy, and the range of melting temperatures. 
  3. Select a desired degenerate primer pair for use in PCR from a list of  
recommendations provided by DD.  The recommendation feature is based on  
user-selected criteria.
  4. Calculate the percentage of primers in the forward and reverse primer  
pools that form stable intramolecular or intermolecular secondary structures.


ABOUT THE AUTHORS:
  Both authors of DD are students at the University of Houston.  Ramin  
Homayouni is a Ph.D. student in the department of Biochemical and Biophysical  
Sciences and Zhong Chen is a senior in the Department of Electrical  
Engineering.   
  DD was created in the summer of 1993 to help us design better primers for use  
in PCR. Of course, the success of any experiment using degenerate oligos  
depends on many factors and is ultimately limited by the nature of the peptide  
sequence.  We feel that DD provides a valuable tool in designing degenerate  
oligos by allowing one to easily examine and compare many potential primers  
from a peptide sequence.
  This is the first version of DD made available to the public, so it is sure  
to have some bugs.  Therefore don't hesitate to let us know about any problems  
that you may be having with the program.  Also, to improve and broaden the  
scope of our program we encourage you to mail us your comments, suggestions, or  
even criticisms to:

e-mail:  Ramin at dna.bchs.uh.edu
Snail-mail:  Ramin Homayouni
             Univ. of Houston, Dept. of Biochemistry
             3201 Cullen, Rm 402 HSC
             Houston, TX 77204-5934


REQUIREMENTS:
  The only hardware required to use DD is a NeXT running NeXTStep 3.0.  The  
authors assume that the user is familiar with using a NeXT machine as well as  
the molecular biology of degenerate primers.


INSTALLATION:
  Fortunately, the NeXTStep environment makes installation extremely easy.   
Just double click on the DegenDesigner.pkg icon. The DD package should include  
the following: 



QUICK START: (for detailed instructions, please refer to the on-line help)

  1. Select the "sequence" button from the MODEL window to input desired  
protein sequence.
  2. Enter your peptide sequence in the SEQUENCE window either manually or by  
importing from the PIR database.
  3. Select the "backtranslate" button in the MODEL window.  DegenDesigner  
displays the sequence of your peptide, the nucleotide sequence corresponding to  
the peptide and the number of degeneracy for each amino acid in the peptide. 
  4. Select the "Forward Primers" button in the MODEL window.  DD lists each  
oligo and its corresponding length, position, degeneracy, and the range of  
melting temperatures.  
  5. Select the "Reverse Primers" button in the MODEL window.  DD lists each  
oligo and its corresponding length, position, degeneracy, and the range of  
melting temperatures.  
  6. To view a list of primer-pair recommendations, click the "recommend"  
button in the PRIMERS window followed by the "OK" button in the RECOMMENDATIONS  
OPTIONS window.  
  7. Select optimization from the menu. To observe the temperature at which the  
selected primers have the least number of stable structures (highest %  
effective primers), select the "Optimal Temperature" button in the OPTIMIZATION  
window.
  8.  Finally, you may generate a report which contains a summary about the  
selected primers.  You can print this document to obtain a hardcopy for future  
reference.





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