SPARSE (Sparsified Prediction and Alignment of RNAs based on their structure Ensembles) is a tool to align RNA sequences based on structural properties of RNA ensembles. The SPARSE algorithm uses a Sankoff-style algorithm and runs in quadratic time without heuristics.
Nucleic acid structure analysis; Sequence analysis
Will S, Otto C, Miladi M, Möhl M, Backofen R "SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics." Bioinformatics 2015; 31(15):2489-96 https://doi.org/10.1093/bioinformatics/btv185
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