SHAPEwarp | SHAPE-guided RNA structural homology search

SHAPEwarp is a Perl library. SHAPEwarp has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

The model-guided search for structurally-homologous RNAs is a non-trivial task, as it largely depends on the quality of the inferred structure model. When it comes to inferring RNA structures from chemical probing data, the challenges are numerous. Use of different chemical probes, or of different approaches for incorporating experimental reactivities as pseudo-free energy contributions can significantly affect the reliability of the inferred RNA structure model. SHAPEwarp is a sequence-agnostic method for the identification of structurally-similar RNA elements in a database of chemical probing-derived reactivity profiles. The approach used by SHAPEwarp is inspired by the BLAST algorithm and builds on top of two widely used methods for similarity search in time series data: Mueen's Algorithm for Similarity Search (MASS) and dynamic time warping (DTW). For support requests, please post your questions to: For a complete documentation, please refer to: