The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for RNA secondary structure analysis. It offers three services: prediction of secondary structure from a single sequence, prediction of the consensus secondary structure for a set of aligned sequences, and design of sequences that fold into a predefined structure. These services are accessible via the Vienna RNA web server at http://rna.tbi.univie.ac.at/. RNA secondary structure prediction is important for understanding RNA function. The Vienna RNA package includes various algorithms for RNA secondary structure prediction and analysis. However, it is primarily designed for Unix command-line users. The web server provides an easy-to-use web interface for less computer-savvy users. The RNAfold server predicts the minimum free energy (mfe) structure of a single sequence using the Zuker and Stiegler algorithm. It can also calculate equilibrium base pairing probabilities using the McCaskill partition function algorithm. The server uses the Turner energy parameters by default, but can also handle DNA sequences. The output includes a static HTML page with the predicted mfe structure and links to plots. Three types of plots can be generated: a conventional secondary structure graph, a dot plot, and a mountain plot. Postscript format is used for structure drawings and dot plots, while SVG is an alternative for interactive visualization. The Alifold server predicts the consensus secondary structure for a set of aligned RNA or DNA sequences using modified dynamic programming algorithms. It supports prediction of mfe structures and pair probabilities. The server accepts Clustal format alignments and limits the size of the upload and alignment length. The Inverse Fold server designs sequences that fold into a predefined structure. It treats sequence design as an optimization problem in sequence space. The server accepts structures in bracket notation and has a maximum length of 100 nt. The server provides basic access to a subset of the functions in the Vienna RNA software package. Future plans include improving visualization and offering standardized data exchange formats for better interoperation with other programs and web services.The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for RNA secondary structure analysis. It offers three services: prediction of secondary structure from a single sequence, prediction of the consensus secondary structure for a set of aligned sequences, and design of sequences that fold into a predefined structure. These services are accessible via the Vienna RNA web server at http://rna.tbi.univie.ac.at/. RNA secondary structure prediction is important for understanding RNA function. The Vienna RNA package includes various algorithms for RNA secondary structure prediction and analysis. However, it is primarily designed for Unix command-line users. The web server provides an easy-to-use web interface for less computer-savvy users. The RNAfold server predicts the minimum free energy (mfe) structure of a single sequence using the Zuker and Stiegler algorithm. It can also calculate equilibrium base pairing probabilities using the McCaskill partition function algorithm. The server uses the Turner energy parameters by default, but can also handle DNA sequences. The output includes a static HTML page with the predicted mfe structure and links to plots. Three types of plots can be generated: a conventional secondary structure graph, a dot plot, and a mountain plot. Postscript format is used for structure drawings and dot plots, while SVG is an alternative for interactive visualization. The Alifold server predicts the consensus secondary structure for a set of aligned RNA or DNA sequences using modified dynamic programming algorithms. It supports prediction of mfe structures and pair probabilities. The server accepts Clustal format alignments and limits the size of the upload and alignment length. The Inverse Fold server designs sequences that fold into a predefined structure. It treats sequence design as an optimization problem in sequence space. The server accepts structures in bracket notation and has a maximum length of 100 nt. The server provides basic access to a subset of the functions in the Vienna RNA software package. Future plans include improving visualization and offering standardized data exchange formats for better interoperation with other programs and web services.