RNAfamily is a simple software tools that enables to display all secondary structures of a family of RNA molecules. It uses the linear backbone representation. RNAfamily provides usual graphical features: zooming, scrolling, etc. Colors of the stems correspond to matching stems. It is also possible to display the nucleotides composing a stem or the whole sequence.
Carnac is a software tool for analysing the hypothetical secondary structure of a family of homologous RNA. It aims at predicting if the sequences actually share a common secondary structure. When this structure exists, Carnac is then able to correctly recover a large amount of the folded stems. The input is a set of single-stranded RNA sequences that need not to be aligned. The folding strategy relies on a thermodynamic model with energy minimization. It combines information coming from locally conserved elements of the primary structure and mutual information between sequences with covariations too.
assp (Assess Secondary Structure Prediction) takes a multiple protein sequence alignmentand estimates the range in accuracy that one can expect for a “perfect” secondary structure prediction made using the alignment.
JPred is a Protein Secondary Structure Prediction server. JPred incorporates the Jnet algorithm in order to make more accurate predictions. In addition to protein secondary structure JPred also makes predictions on Solvent Accessibility and Coiled-coil regions (Lupas method).
NetSurfP predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method also simultaneously predicts the reliability for each prediction, in the form of a Z-score. The Z-score is related to the surface prediction, and not the secondary structure.