RNApasta: Statistics and editing of RNA multiple structural alignments


RNApasta is RNApasta is a Java application to calculate a variety of useful statistics related to RNA stem-loop and pseudoknot structures. It will also perform functions related to alignment editing. The input data may be in a "pasta" formatted file, a variant of the fasta format, or in a Stockholm formatted files as downloaded from the Rfam database.


RNApasta is coded in Java and has been tested on Windows, Linux, and MacOS computers. It is available either as a precompiled java archive file (.jar) which is ready to run, or as source code which can be compiled.


  • [Malmberg, et al, 2010] Malmberg, R., Shaw, T., and Cai, L. (2010) RNApasta: a tool for analysis of RNA structural alignments, Journal of Bioinforamtics Research and Applications, accepted.