RFMapp: ribosome flow model application

Abstract

The RFMapp is a graphical user interface application based on the RFM (ribosome flow model), enabling the estimation of the translation elongation rates of messenger ribonucleic acids (mRNAs) and the profile of ribosomal densities along the mRNAs, in a computationally efficient way. The RFMapp is based on the approach previously described by Reuveni et al., and unlike other traditional approaches in the field, which are mainly related to the genes' mean codon translation efficiency, the RFM additionally considers the codon order, the ribosomes' size and their order. Thus, it has been shown that RFM outperforms traditional predictors when analyzing both heterologous and endogenous genes. Distributable cross-platform application and guideline are available for download at: http://www.cs.tau.ac.il/~tamirtul/RFM_Installers/install.htm.