ExtRamp Online: Enabling ramp sequence calculations via an intuitive web interface.

Abstract

Motivation: Ramp sequences are an understudied evolutionarily-conserved mechanism for regulating protein translational efficiency. Slowly-translated codons concentrated at the 5' end of genes form ramp sequences that counterintuitively increase overall translational efficiency by evenly spacing ribosomes at initiation, which limits downstream ribosomal collisions. We previously developed ExtRamp, which is the only algorithm to identify translational ramp sequences in single genes. ExtRamp currently lacks a web interface to facilitate wider adoption and application for non-programmers. Additionally, ExtRamp currently identifies ramp sequences using only species-wide codon efficiencies that may lack the specificity of tissue and cell type-specific codon usage biases.Results: We present an online interface for ExtRamp to facilitate wider adoption and application for non-programmers, along with a significant improvement to the underlying algorithm to calculate tissue and cell type-specific ramp sequences (https://ramps.byu.edu/ExtRampOnline). ExtRamp Online contains all options available in the original ExtRamp algorithm with additional pre-set default values to enable researchers to calculate human tissue-specific or genome-wide ramp sequences on any web browser. Human tissue and cell type-specific codon usage biases have been precomputed and can be applied with a simple drop-down menu. Hover-over hints provide users with detailed information on all available options, which will help facilitate future creative analyses using ramp sequences. Availability: ExtRamp Online is publicly available at https://ramps.byu.edu/ExtRampOnline. All associated scripts are publicly available at https://github.com/ridgelab/ExtRampOnline.