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 ______________|____________________
