This is the Linux app named mCarts whose latest release can be downloaded as mCarts.v1.2.0.tgz. It can be run online in the free hosting provider OnWorks for workstations.
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Many RBPs recognize very short and degenerate sequences, with targeting specificity achieved by mechanisms such as synergistic binding to multiple clustered sites and modulation of site accessibility through different RNA-secondary structures. mCarts integrates the number and spacing of individual motif sites, their accessibility and conservation, which substantially improves signal to noise ratio. This algorithm learns and quantifies rules of these features, taking advantage of a large number of in vivo RBP binding sites obtained from high throughput sequencing of RNAs isolated by cross-linking and immunoprecipitation (HITS-CLIP). We applied this algorithm to study two representative RBPs, Nova and Mbnl. Despite the very low information content in individual motif elements, our algorithm made very specific predictions for successful experimental validation.
Science/Research, Advanced End Users
This is an application that can also be fetched from https://sourceforge.net/projects/mcarts/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.