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shapemapper website  

Mutational profiling (MaP) has become perhaps the most accurate and certainly most direct way of reading out chemical modifications in nucleic acids. ShapeMapper 2 is a completely rewritten version of our software for reading out the results of an RNA chemical probing experiment by massively parallel sequencing. ShapeMapper 2 integrates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings to now identify RNA adduct sites as accurately as achieved by careful manual analysis of electrophoresis data, the prior highest-accuracy standard. ShapeMapper 2 can be used to read out SHAPE, DMS, RING, and many other classes of experiments.

Environment Modules

Run module spider shapemapper to find out what environment modules are available for this application.

System Variables

  • HPC_SHAPEMAPPER_DIR - installation directory
  • HPC_SHAPEMAPPER_BIN - executable directory
  • HPC_SHAPEMAPPER_DOC - documentation directory
  • HPC_SHAPEMAPPER_EXE - test data directory


If you publish research that uses shapemapper you have to cite it as follows:

S. Busan and K.M. Weeks, Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2. RNA 23, asap available (2017).