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Welcome to the Webserver for Aligning structural RNAs. This server utilizes several tools simultaneously to align and predict the common secondary structure of multiple RNA sequences.

Input multiple sequences in FASTA format:

OR specify a file (FASTA format):

Example output -- Example input -- Dataset used in paper

Which programs would you like to run:

CMfinder FoldalignM LaRA LocARNA MASTR
MXSCARNA Murlet RNASampler Stral+PETfold RNAcast+RNAforester
ClustalW+Pfold ClustalW+RNAalifold MAFFT+Pfold MAFFT+RNAalifold

Do local alignment

[OPTIONAL] A reference alignment with structure in Stockholm format or a FASTA-like format

[OPTIONAL] Please name your submission (whitespaces will be replace with "_")

Please provide an E-mail address for receiving the results:

Please send any comments or report bugs to Elfar Torarinsson or Stinus Lindgreen