In article <55nc61$q9e at c4.hrz.uni-giessen.de>,
schlaude at paul.bio.uni-giessen.de (Gerd Schlauderer) writes:
>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.
Did you try a dotplot? just my 0.02.
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