A: Primer design: Is there a source of statistical base distributions in genomes?

[Stefan Unger]

RightPrimer calculates a score _both_ for own gene and for genome. Thanks 
for your interest.

Wolfgang Schechinger (u7k0201 at sunmail.lrz-muenchen.de) wrote:
: sunger at crl.com (Stefan Unger) wrote:
: >The MAC program RightPrimer already does this and is very reasonably 
: >priced.  Send mailing address if you would like information.  I am a dealer.  
: >Thanks.
: >
: >Wolfgang Schechinger 
: >(u7k0201 at sunmail.lrz-muenchen.de) wrote: : Hello everyone!
: >
: >: Primer sequences should only match to the targetted sequence. That sounds simple, but how to 
: >: prove it? OK, you can search the GenBank for another match, but the GenBank yet is not complete 
: >: (will it ever be?). I have heard about a method by mathematically deriving the probabilities of 
: >: certain sequences from the real distribution of small fragments (e.g dimers, tetramers or 
: >: hexamers) in a genome. 
: >: To compile these data sets I suppose there's a need of much workspace and machine capacity. 
: >: Thus I would like to know if this approach makes sense and is really neccessary and, if so,
: >: if there already exists some data on the issue - where may it be found?
: >
: >: Thank you for your help!
: >: Please email your posting, too.
: >
: >: -- 
: >: +++++++++++++++++++++++++++++++++++++++++++
: >: Wolfgang Schechinger
: >: [cut off, see below!]
: >
: >: (Standard disclaimer applies)
: >: +++++++++++++++++++++++++++++++++++++++++++
: >
: >
: Dear Stefan, Thank you for your reply! 
: Testing my primer for another match on my gene is not the actual problem. Maybe I didn't point 
: that out clearly enough. I'm looking for a way of optimizing my primers for minimal match on 
: THE REST OF THE GENOME (OR mRNA/cDNA). 

: -- 
: +++++++++++++++++++++++++++++++++++++++++++
: Wolfgang Schechinger
: Institute for Diabetes Reserch 
: Koelner Platz 1
: 80804 Munich
: Germany 
: Phone +49 (89) 30 79 31 24
: Fax   +49 (89) 30 81 733
: email u7k0201 at sunmail.lrz-muenchen.de

: (Standard disclaimer applies)
: +++++++++++++++++++++++++++++++++++++++++++