alteRNA: RNA Density Fold

alteRNA is an alternative to many RNA folding methods. It takes an RNA sequence and computes its single secondary structure. Using dynamic programming, it minimizes a linear combination of energy density and the total free energy.

inteRNA: RNA-RNA Interaction Prediction

inteRNA predicts the joint secondary structure of two RNA sequences.

piRNA: RNA-RNA Interaction Partition Function

piRNA predicts the joint partition function, equilibrium concentration, ensemble energy, and melting temperature for two RNA sequences.

pRuNA: RNA Interaction Search Engine

pRuNA is a sequence based pruning technique that eliminates a significant fraction of a Non coding RNA (ncRNA) data set and retains only the most likely ncRNA candidates for forming a stable joint structure with the query mRNA.

smyRNA: novel ab initio ncRNA finder

smyRNA is a platform independent C program aiming to discover novel ncRNAs in a given genome using previously annotated ncRNAs.

Please contact rsalaris@cs.sfu.ca for comments and questions.