The MSARi (Multiple Sequence Alignments for Statistical Detection of RNA Secondary Structure) program indentifies conserved RNA secondary structure in non-coding RNA genes and mRNAs by searching multiple sequence alignments of a large set of candidate catalogs for correlated arrangements of reverse-complementary regions
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Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12102-7. Epub 2004 Aug 10.
MSARI: multiple sequence alignments for statistical detection of RNA secondary structure.
Coventry A, Kleitman DJ, Berger B.