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NAMElocarna-motif-scan SYNOPSISlocarna-motif-scan [options] <motif> <seq> ATTENTION: some options undocumented Options: --help brief help message --man full documentation --verbose be verbose --quiet be quiet <motif> a dp file describing your motif <seq> a fasta file containing the sequence(s) DESCRIPTIONThe program scans for a match of a RNA "motif", given by a (multiple) alignment in a possibly long stretch of D/RNA We use a sliding window, fold each window with RNALfold -p and search for k-best locarna hits in the window The K-best hits are recorded
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