I am using PCR to detect and identify phytopathogenic bacteria. For this
purposes we used conserved regions of several genes of a family.
I was looking for a software to be used on this several genes but the
programs I know (primer, Oligo) are not able to usealigned sequences.
During this time I heard somebody using a non-thermodynamical approach
to look for primers (but helas not from aligned sequences). This program
use a table of the frequent and rare octamers of an organism (e.g Homo sapiens)
and look in the submitted sequence for the less frequent octamers of the
organism present (s) in the studied sequence.
My question is: does anyone know some references/articles about the
conservation of e.g. octamers (or shorter or longer oligonucleotides) in
the several kingdoms and more particularly in the plants?
This software looks very nice (under Windows 3.X on PC) but is yet not
commercialy available (maybe in a few months) and does not get tables of
frequencies for plants...
Any help appreciated...
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