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LOCARNA_RNAFOLD_PP(1) User Commands LOCARNA_RNAFOLD_PP(1) NAME locarna_rnafold_pp - manual page for locarna_rnafold_pp (LocARNA 2.0.0) DESCRIPTION locarna_rnafold_pp -- compute RNA pair probabilities and write in pp-format USAGE: locarna_rnafold_pp [options] Folds RNA sequences by calling the Vienna RNA library and directly writes LocARNA's pp 2.0 format. In many cases this program can replace a call to RNAfold or RNAalifold followed by a conversion of its output to pp format. mlocarna uses this script wherever possible. This tool allows moreover pre- computing "in-loop" probabilities as used by SPARSE and ExpaRNA-p. OPTIONS -h, --help Help -V, --version Version info -v, --verbose Verbose -C, --use-struct-constraints Use structural constraints --noLP No lonely pairs --maxBPspan=<span>(-1) Limit maximum base pair span (default=off) --stacking Compute stacking terms --dangling=<param>(2) Dangling option value --in-loop Compute in-loop probabilities -p, --min-prob=<prob>(0.001) Minimal probability --p_unpaired_in_loop=<threshold>(0.0005) Threshold for prob_unpaired_in_loop --p_basepair_in_loop=<threshold>(0.0005) Threshold for prob_basepair_in_loop -o, --output=<filename>() Output file --force-alifold Force alifold for single sequences locarna_rnafold_pp (LocARNA 2.0.0) July 2024 LOCARNA_RNAFOLD_PP(1)
NAME | DESCRIPTION | OPTIONS
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