Software/Method to determine an antisense RNA

Gerd Schlauderer schlaude at paul.bio.uni-giessen.de
Tue Nov 5 07:33:05 EST 1996


We want to construct an anti-sense RNA to suppress the expression of a
protein. Is there a program to check, which sequence parts are not
involved in stem-loops? 

RNA-folding programs like mfold are not feasible for this problem,
because the RNA is too large (about 5000 bases). Is it practable to run 
fasta using a sequencewindow of 20 bases as query and the complementary 
RNA-sequence as database? The lowest scoring sequences should be
ideal for anti-sense RNA binding.

Regards,

      Gerd

-- 
Dr. Gerd Schlauderer --------------------------|-------------------    
Institut f. Mikrobiologie u. Molekularbiologie |  Tel.: 0641-7029646  
Frankfurterstr. 107              35392 Giessen |  FAX.: 0641-7029659
schlaude at paul.bio.uni-giessen.de ______________|____________________






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