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.
BSpred is a neural network based algorithm for predicting binding site of proteins from amino acid sequences. The algorithm was extensively trained on the sequence-based features including protein sequence profile, secondary structure prediction, and hydrophobicity scales of amino acids.
DPS (Drug Pair Seeker) is a Java program that attempts to predict and prioritize pairs of drugs using the Connectivity Map dataset. Users can enter lists of up and down differentially expressed genes from their experiments to receive a ranked list of drug combinations that are predicted to either reverse or aggravate the gene expression state of the cells or tissue of interest using a simple formula.
DriverNet is a package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph, which is a gene-gene interaction network deduced from pathway data. A greedy algorithm is used to find the possible driver genes, which may mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.