Translational efficiency detection software tools | Transcription data analysis
Translation has been the subject of intense modelling efforts in the last five decades, using various mathematical and computational approaches. These models aimed at predicting protein production rates and understanding the role of mRNA features or contributions of translation stages.
Infers the species-specific tRNA Adaptation Index (tAI) wobble weights. Stalcalc is an online tool that provides the tAI value of the sequence as well as the normalized tAI values of each coding codon in the selected genome. It includes 100 different species from the three domains of life, along with an option to download a standalone software package of the stAIcalc that calculates tAI with species-specific weights for new organisms not included in the list.
Assists users in constructing atomic models from experimental data. MDfit is a computational methodology that allows users to incorporate information from x-ray crystallography, cryo-em and biochemical studies in order to prepare atomic models for these configurations. It uses gromacs molecular dynamics simulation code. This method was used to obtain all-atom models for configurations of macromolecular complexes.
A model trained on experimental imaging-derived data, able to quickly and accurately predict the steady state number of ribosomes per transcript in entire transcriptomes. RiboAbacus uses a mechanistic model of ribosome dynamics, enabling the quantification of the relative importance of different features (such as codon usage and the 5' ramp effect) in determining the accuracy of predictions. The model has been optimized in the human Hek-293 cell line to fit thousands of images of human polysomes obtained by atomic force microscopy, from which we could get a reference distribution of the number of ribosomes per mRNA with unmatched resolution. RiboAbacus is an intuitive tool that allows an immediate estimation of crucial translation properties for entire transcriptomes, based on easily obtainable transcript expression levels.
Supplies a deterministic model of protein synthesis. The PURE system simulator is a model which consists of more than 240 components, and about 900 reactions can be used to reproduce Met-Gly-Gly tripeptiide (fMGG) synthesis. This method leans on the exploitation of ordinary differential equations (ODE) coupled to items derived from an Escherichia coli-based reconstituted in vitro translation system.
Allows users to extract ramp sequence based on the tRNA adaptation index or relative codon adaptiveness. ExtRamp includes several filters facilitating the analysis of codon and enabling identification of genes with a ramp sequence. This tool was used for detecting areas of decreased translational efficiency at the start of individual genes or any other codon table.