SHAPEwarp is a sequence-agnostic method for the SHAPE-guided search of RNA regions sharing structural similarity, in a database of SHAPE reactivity profiles.
The algorithm builds on a concept very similar to that used by the popular BLAST algorithm for sequence similarity search. Kmer search is performed using the
MASS algorithm, while kmer extension exploits an approach that combines both features of Dynamic Time Warping and Gotoh's alignment algorithm.
For additional information, please refer to the paper.
DRACO (Deconvolution of RNA Alternative COnformations) is an algorithm for the reconstruction of RNA structural ensembles from mutational profiling (MaP) experiments. By coupling spectral deconvolution and fuzzy clustering, DRACO can identify the number of coexisting RNA conformations, their relative stoichiometries, and reconstruct their individual reactivity profiles. For additional information, please refer to the paper.
RNA Framework is an all-in-one toolkit for the analysis of most NGS-based RNA structure probing and post-transcriptional modification mapping experiments.
It can handle most methods for querying RNA secondary structures, either based on RT drop-off (CIRS-seq, SHAPE-seq, Structure-seq, DMS-seq, PARS, etc.) or on mutational profiling (SHAPE-MaP, DMS-MaPseq, etc.),
and RNA post-transcriptional modification mapping approaches, either immunoprecipitation-based (m1A, m6A, m5C, hm5C, etc.) or single-base resolution (Ψ, 2'-OMe, etc.).
For additional information, please refer to the paper.